Repetitive transcranial magnetic stimulation in the treatment of resistant depression: changes of specific neurotransmitter precursor amino acids.

Repetitive transcranial magnetic stimulation (rTMS) for treatment-resistant major depression offers an alternative therapy, since more than every third patient is not responding to adequate antidepressive treatment. In this interventional study safety, symptom development and changes of serum concentrations of neurotransmitter precursor amino acids, of immune activation and inflammation markers, of brain-derived neurotrophic factor (BDNF), nitrite as well as of salivary amylase were measured before and after a frontal polar cortex stimulation using rTMS as add-on treatment in 38 patients with treatment-resistant depression. Out of these, 17 patients received sham stimulation as a control. Treatment was well tolerated: with the exception of one patient of the verum group, who described discomfort during the second treatment, no serious adverse effects were observed. Improvement of depression with a significant decrease in the HAMD-7 scale (p = 0.001) was found in patients treated with rTMS, but not in sham-treated patients. Furthermore, serum phenylalanine and tyrosine dropped significantly (p = 0.03 and p = 0.027, respectively) in rTMS-treated patients. The kynurenine to tryptophan ratio (Kyn/Trp) tended to decrease under rTMS (p = 0.07). In addition, associations between concentrations of BDNF and neopterin as well as serum nitrite levels were found in patients after rTMS treatment, which indicates an influence of immune regulatory circuits on BDNF levels. In the sham-treated patients, no changes of biomarker concentrations were observed. Results show that rTMS is effective in the treatment of resistant depression. rTMS appears to influence the enzyme phenylalanine hydroxylase, which plays a central role in the biosynthesis of neurotransmitter precursors tyrosine and dihydroxyphenylalanine (DOPA).

Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease.

Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.

Built-up area and population density: Two Essential Societal Variables to address climate hazard impact.

Scientists use Essential Climate Variables to understand and model the Earth's climate. Complementary to the Climate Variables this paper introduces global built-up area and population density, referred to as Essential Societal Variables, that can be used to model human activities and the impact of climate induced hazards on society. Climate impact scenarios inform policy makers on current and future risk and on the cost for mitigation and adaptation measures. The global built-up area and global population densities are generated from Earth observation image archives and from national population census data in the framework of the Global Human Settlement Layer (GHSL) project. The layers are produced with fine granularity for four epochs: 1975, 1990, 2000 and 2015, and will be updated on a regular basis with open satellite imagery. The paper discusses the relevance of global built-up area and population density for a number of policy areas, in particular to understand regional and global urbanization processes and for use in operational crisis management and risk assessment. The paper also provides examples of global statistics on exposure to natural hazards based on the two ESVs and their use in policy making. Finally, the paper discusses the potential of using population and built-up area for developing indicators to monitor the progress in Agenda 2030 including the Sustainable Development Goals (SDGs).

Plasticity-related genes in brain development and amygdala-dependent learning.

Learning about motivationally important stimuli involves plasticity in the amygdala, a temporal lobe structure. Amygdala-dependent learning involves a growing number of plasticity-related signaling pathways also implicated in brain development, suggesting that learning-related signaling in juveniles may simultaneously influence development. Here, we review the pleiotropic functions in nervous system development and amygdala-dependent learning of a signaling pathway that includes brain-derived neurotrophic factor (BDNF), extracellular signaling-related kinases (ERKs) and cyclic AMP-response element binding protein (CREB). Using these canonical, plasticity-related genes as an example, we discuss the intersection of learning-related and developmental plasticity in the immature amygdala, when aversive and appetitive learning may influence the developmental trajectory of amygdala function. We propose that learning-dependent activation of BDNF, ERK and CREB signaling in the immature amygdala exaggerates and accelerates neural development, promoting amygdala excitability and environmental sensitivity later in life.

Systematic review: bile acids and intestinal inflammation-luminal aggressors or regulators of mucosal defence?

BACKGROUND: Inflammatory bowel diseases (IBD), comprising Crohn's disease and ulcerative colitis (UC), are chronic conditions attributed to an aberrant immune response to luminal triggers. Recently, published work suggests a pathogenic role for bile acids in this context. AIM: To perform a systematic review of studies investigating the role of bile acids in intestinal inflammation and present potentially relevant clinical implications. METHODS: Pubmed search for English language articles published up to May 2015. Terms used were: 'bile', 'bile acid', 'barrier', 'small bowel injury', 'Crohn's' and 'colitis'. RESULTS: Experimental studies support a variable role for bile acids in intestinal barrier homoeostasis. This may be attributed to different physicochemical properties, variable effects on epithelia and immune cells via bile acids-specific receptors, or through a cross-talk with the gut microbiome. A reduction in the bile acids pool, with lower concentrations of secondary forms, has been recognised for some time in Crohn's disease and associated to ileal dysfunction and bile acids malabsorption. Recent work suggests that these changes, including an increase in sulphated forms, are related to inflammatory activity in both Crohn's disease and UC. The detrimental effects of 'western diet' elements such as emulsifiers and fat, which have been implicated in the development of the current IBD and obesity epidemics, may also be bile acid-mediated. CONCLUSIONS: Although there are only a few observational clinical studies to support an interaction, in vivo human and animal studies support an association between bile acids metabolism, the gut microbiome and intestinal inflammation. This may well prove to have significant diagnostic and therapeutic implications.

Antidepressants and anti-inflammatory drugs differentially reduce the release of NGF and BDNF from rat platelets.

INTRODUCTION: Platelets store serotonin and brain-derived neurotrophic factor (BDNF) as well as amyloid precursor protein and nerve growth factor (NGF), thus platelets are of special interest in depression and Alzheimer's disease, respectively. Both diseases are associated with inflammation and release of NGF or BDNF from platelets may play a potent role. METHODS: Platelets were isolated from adult Sprague-Dawley rats and were incubated with anti-inflammatory drugs (ibuprofen and indomethacin) and antidepressants (citalopram, paroxetine and sertraline) (final concentration: 0.3 µM) with or without 2 mM calcium chloride. The release of NGF and BDNF was analyzed in comparison to serotonin release from rat platelets after 10 or 60 min. RESULTS: Spontaneous release of serotonin and BDNF was approximately 10-15% of total serotonin or BDNF content in platelets, but nearly all NGF was released within 10 min. All antidepressants increased the serotonin release from rat platelets. NGF release was reduced by sertraline, paroxetine and ibuprofen, but only when calcium was present, except for sertraline after 10 min. BDNF release was only reduced by ibuprofen when calcium was added. CONCLUSION: We conclude that antidepressants and anti-inflammatory drugs differentially influence the NGF and BDNF release, in a time-, dose- and calcium-specific pattern.

Postnatal development of electrophysiological properties of principal neurons in the rat basolateral amygdala.

The basolateral amygdala (BLA) is critically involved in the pathophysiology of psychiatric disorders, which often emerge during brain development. Several studies have characterized postnatal changes to the morphology and biochemistry of BLA neurons, and many more have identified sensitive periods of emotional maturation. However, it is impossible to determine how BLA development contributes to emotional development or the aetiology of psychiatric disorders because no study has characterized the physiological maturation of BLA neurons. We addressed this critical knowledge gap for the first time using whole-cell patch clamp recording in rat BLA principal neurons to measure electrophysiological properties at postnatal day (P)7, P10, P14, P21, P28 and after P35. We show that intrinsic properties of these neurons undergo significant transitions before P21 and reach maturity around P28. Specifically, we observed significant reductions in input resistance and membrane time constant of nearly 10-and 4-fold, respectively, from P7 to P28. The frequency selectivity of these neurons to input also changed significantly, with peak resonance frequency increasing from 1.0 Hz at P7 to 5.7 Hz at P28. In the same period, maximal firing frequency significantly increased and doublets and triplets of action potentials emerged. Concomitantly, individual action potentials became significantly faster, firing threshold hyperpolarized 6.7 mV, the medium AHP became faster and shallower, and a fast AHP emerged. These results demonstrate neurons of the BLA undergo vast change throughout postnatal development, and studies of emotional development and treatments for juvenile psychiatric disorders should consider the dynamic physiology of the immature BLA.

Effects of long-term moderate ethanol and cholesterol on cognition, cholinergic neurons, inflammation, and vascular impairment in rats.

There is strong evidence that vascular risk factors play a role in the development of Alzheimer's disease (AD) or vascular dementia (vaD). Ethanol (EtOH) and cholesterol are such vascular risk factors, and we recently showed that hypercholesterolemia causes pathologies similar to AD [Ullrich et al. (2010) Mol Cell Neurosci 45, 408-417]. The aim of this study was to investigate the effects of long-term (12 months) EtOH treatment (20% v/v in drinking water) alone or long-term 5% cholesterol diet alone or a combination (mix) in adult Sprague-Dawley rats. Long-term EtOH treatment (plasma EtOH levels 58±23 mg/dl) caused significant impairment of spatial memory, reduced the number of choline acetyltransferase- and p75 neurotrophin receptor-positive nucleus basalis of Meynert neurons, decreased cortical acetylcholine, elevated cortical monocyte chemoattractant protein-1 and tissue-type plasminogen activator, enhanced microglia, and markedly induced anti-rat immunoglobulin G-positive blood-brain barrier leakage. The effect of long-term hypercholesterolemia was similar. Combined long-term treatment of rats with 20% EtOH and 5% cholesterol (mix) did not potentiate treatment with EtOH alone, but instead counteracted some of the EtOH-associated effects. In conclusion, our data show that vascular risk factors EtOH and cholesterol play a role in cognitive impairment and possibly vaD.

Non-cycloplegic refractive screening can identify infants whose visual outcome at 4 years is improved by spectacle correction.

The Second Cambridge Population Infant Vision Screening Programme using the VPR-1 videorefractor without cycloplegia was undertaken in order to identify those infants with refractive errors who were potentially amblyogenic or strabismogenic. Infants identified at eight months were entered into a control trial of treatment with partial spectacle correction and underwent a long-term follow-up that monitored a wide range of visual, visuoperceptual, visuocognitive, visuomotor, linguistic and social development. In the present paper, the authors report on the outcome measures of visual acuity and strabismus. Poor acuity was defined as a best-corrected acuity of 6/12 or worse on crowded letters or 6/9 or worse on single letters, at age 4 years. Acuity was measured in 79 infants who were significantly hyperopic and/or anisometropic at 11-12 months of age, 23 who showed hyperopia of +3D but less than +3.5D, 196 control subjects, 14 controls with refractive errors, and 126 others who showed an accommodative lag on screening but were not significantly hyperopic on first retinoscopy. There was a poorer acuity outcome in the untreated group of hyperopes compared to controls (p < 0.0001) and to the children who were compliant in spectacle wear (p < 0.001) or who were prescribed spectacles (p < 0.05). Children who were significantly hyperopic at eight months were also more likely to be strabismic by 5.5 years compared to the emmetropic control group (p < 0.001). However, the present study did not find a significant difference in the incidence of strabismus between corrected and uncorrected hyperopic infants. Children who were not refractively corrected for significant hyperopia were four times more likely to have poor acuity at 5.5 years than infants who wore their hyperopic correction, supporting the findings of the First Cambridge Population Infant Vision Screening Programme.

Identification of a phosphofructokinase-encoding gene from Streptococcus thermophilus CNRZ1205--a novel link between carbon metabolism and gene regulation?

In order to isolate genes encoding so-called Two-Component Regulatory Systems from the lactic acid bacterium Streptococcus thermophilus, a cloning strategy was employed based on suppression of the alkaline phosphatase-negative phenotype displayed by the Escherichia coli strain ANCC22. Several suppressing clones were obtained which were shown to produce alkaline phosphatase activity. Sequence analysis of four of these clones revealed the presence of overlapping DNA inserts representing two ORFs, designated pfkT and pykT, whose deduced protein products exhibit significant similarity to phosphofructokinases and pyruvate kinases, respectively, from a variety of bacteria. A plasmid bearing pfkT was shown to complement a phosphofructokinase-negative mutant of E. coli, showing that this gene indeed specifies phosphofructokinase activity. It was shown that suppression of the alkaline phosphatase-negative phenotype of E. coli ANCC22 due to the presence of pfkT is caused by modulation of the intracellular level of acetyl phosphate.

Shear-induced degradation of linear polyacrylamide solutions during pre-electrophoretic loading.

Electrophoretic channels are filled with a polymer matrix prior to their use in DNA separations. This process, called gel-loading, can be accomplished manually, using syringes, or can be automated through the use of small pumps or vacuum. The injection rate is constrained by the desire to minimize shear-induced degradation of the polymer molecules. Currently, the community lacks quantitative data with which to gauge the range of flow rates that prevent polymer degradation. In this study, measurements of the zero shear rate viscosity of linear polyacrylamide (LPA) solutions are used to determine the LPA molecular weight before and after gel-loading. The results indicate molecular degradation in polymer solutions even when injected at minimal flow rates of 1 microL/min. To correlate these rheological observations of shear-induced degradation with subsequent electrophoretic performance, the degraded solutions were used as sieving matrixes for DNA sequencing analysis. The decreases in electrophoretic resolution and increases in peak widths between sheared and nonsheared LPA solutions are related to the degradation in molecular weight experienced by the polymer solutions.

A closed-cycle capillary polymerase chain reaction machine.

A novel thermocycling machine based on a microcapillary equipped with bidirectional pressure-driven flow and in situ optical position sensors is described. A 1-microL droplet of reaction mixture moves between three heat zones in a 1-mm-i.d., oil-filled capillary using a multielement scattered light detector and active feedback. Dwell times and accelerations can be adjusted independently. As a demonstration of the device, 30 cycles of a 500-base pair product were performed in 23 min with 78% amplification efficiency. This result compares well with previous high-speed thermocyclers. Theoretically, the arrangement can approach a time of 2.5 min for 30 cycle amplifications of a 500-base pair product.

Neural measurement of sound duration: control by excitatory-inhibitory interactions in the inferior colliculus.

In the inferior colliculus (IC) of the big brown bat, a subpopulation of cells ( approximately 35%) are tuned to a narrow range of sound durations. Band-pass tuning for sound duration has not been seen at lower levels of the auditory pathway. Previous work suggests that it arises at the IC through the interaction of sound-evoked, temporally offset, excitatory and inhibitory inputs. To test this hypothesis, we recorded from duration-tuned neurons in the IC and examined duration tuning before and after iontophoretic infusion of antagonists to gamma-aminobutyric acid-A (GABA(A)) (bicuculline) or glycine (strychnine). The criterion for duration tuning was that the neuron's spike count as a function of duration had a peak value at one duration or a range of durations that was >/=2 times the lowest nonzero value at longer durations. Out of 21 units tested with bicuculline, duration tuning was eliminated in 15, broadened in two, and unaltered in four. Out of 10 units tested with strychnine, duration tuning was eliminated in four, broadened in one, and unaltered in five. For units tested with both bicuculline and strychnine, bicuculline had a greater effect on reducing or abolishing duration tuning than did strychnine. Bicuculline and strychnine both produced changes in discharge pattern. There was nearly always a shift from an offset response to an onset response, indicating that in the predrug condition, inhibition arrived simultaneously with excitation or preceded it. There was often an increase in the length of the spike train, indicating that in the predrug condition, inhibition also coincided with later parts of excitation. These findings support two hypotheses. First, duration tuning is created in the IC. Second, although the construction of duration tuning varies in some details among IC neurons, it follows three rules: 1) an excitatory and an inhibitory event are temporally linked to the onset of sound but temporally offset from one another; 2) the duration of some inhibitory event must be linked to the duration of the sound; 3) an excitatory event must be linked to the offset of sound.

Optimization of high-performance DNA sequencing on short microfabricated electrophoretic devices.

We have examined the parametric performance of short microfabricated electrophoresis devices that operate with a replaceable linear poly(acrylamide) (LPA) solution for the application of DNA sequencing. A systematic study is presented of the dependence of selectivity, separation efficiency, and resolution of sequencing fragments on buffer composition, LPA concentration, LPA composition, microdevice temperature, electric field, and device length. A specific optimization is made for DNA sequencing on 11.5-cm devices. Using a separation matrix composed of 3.0% (w/w) 10 MDa plus 1.0% (w/w) 50 kDa LPA, elevated microdevice temperature (50 degrees C), and 200 V/cm, high-speed DNA sequencing of 580 bases on standard M13mp18 was obtained in only 18 min with a base-calling accuracy of 98.5%. Read lengths of 640 bases at 98.5% accuracy were achieved in approximately 30 min by reducing the electric field strength to 125 V/cm. We believe that this constitutes matrix-limited performance for microdevices of this length using LPA sieving matrix and this buffer chemistry. In addition, it was confirmed, that shorter devices are rather impractical for production sequencing applications when LPA is used as sieving matrix.

Eight hundred-base sequencing in a microfabricated electrophoretic device.

The human genome will be sequenced using capillary array electrophoresis technology. Although currently achieving only 550 base reads per run, capillary arrays have increased the efficiency and lowered the cost of sequencing by eliminating gel plate preparation, reducing sample volumes, and offering automation and speed. However, much higher throughput and greater cost reductions are needed. The next major advancement in sequencing technology is expected from the development of arrays of microfabricated channels in a plate or "chip" format. For de novo sequencing, the practical utility of the microdevice approach has been limited by device length to a read of 500-600 bases per run. We demonstrate a significant milestone for a microfabricated device by obtaining an average read length of 800 bases in 80 min (98% accuracy) for either M13 standards or DNA sequencing samples from the Whitehead Institute Center for Genomic Research (WICGR) production line. This result is achieved in 40-cm-long channels using a new class of large-scale microfabricated devices. Both microfabrication of extended structures and achievement of long reads are essential steps toward a 384-lane very-large-scale microfluidic (VLSMF) system for ultrahigh-throughput DNA sequencing analysis, currently under construction in our laboratory.

Microchip electrophoresis: a method for high-speed SNP detection.

As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality factors as good as conventional electrophoresis in approximately 100 s. This is 10 and 50 times faster than capillary and slab gel electro-phoresis, respectively. The method was highly accurate with an average error of mutation site measurement of only +/-5 bp. No clean-up of the digestion mixtures was needed prior to injection. This greatly simplifies sample handling relative to capillary instruments, which is important for high-throughput screening applications. Following identification, absolute mutation determination of the screened samples was achieved in a second microdevice optimized for four-color DNA sequencing. Total run time was 25 min in this second device and sequencing data were in full agreement with ABI Prism 377 sequencing runs which required 3.5 h. The tandem application of microdevices for location then full characterization of SNPs appears to confirm many of the improvements claimed for future application of microdevices in practical scaled screening for mutational analysis.

Recent developments in DNA sequencing by capillary and microdevice electrophoresis.

The present review covers papers published in the years 1997 and 1998 on DNA sequencing by capillary and microdevice electrophoresis. The article does not include other electrophoretic DNA applications such as analysis of oligonucleotides, genotyping, and mutational analysis. Capillary gel electrophoresis (CGE) is starting to become a viable competitor to slab gel electrophoresis for DNA sequencing. Commercially available multicapillary array sequencers are now entering sequencing facilities which to date have totally relied on traditional slab gel technology. CGE research on DNA sequencing therefore becomes increasingly concerned with the critical task of fine-tuning the operational parameters to create robust sequencing systems. Electrophoretic microdevices are being considered the next technological step in DNA sequencing by electrophoresis.

Toward real-world sequencing by microdevice electrophoresis.

We report results using a microdevice for DNA sequencing using samples from chromosome 17, obtained from the Whitehead Institute Center for Genome Research (WICGR) production line. The device had an effective separation distance of 11.5 cm and a lithographically defined injection width of 150 microm. The four-color raw data were processed, base-called by the sequencing software Trout, and compared to the corresponding ABI 377 sequence from WICGR. With a criteria of 99% accuracy, we achieved average continuous reads of 505 bases in 27 min with 3% linear polyacrylamide (LPA) at 150 V/cm, and 460 bases in 22 min with 4% LPA at 200 V/cm at a temperature of 45 degrees C. In the best case, up to 565 bases could be base-called with the same accuracy in <25 min. In some instances, Trout allowed for accurate base-calling down to a resolution R as low as R = 0.35. This may be due in part to the high signal-to-noise ratio of the microdevice. Unlike many results reported on capillary machines, no additional sample cleanup other than ethanol precipitation was required. In addition, DNA fragment biasing (i.e., discrimination against larger fragments) was reduced significantly through the unique sample injection mechanism of the microfabricated device. This led to increased signal strength for long fragments, which is of great importance for the high performance of the microdevice.