Directed cortical information flow during human object recognition: analyzing induced EEG gamma-band responses in brain's source space

The increase of induced gamma-band responses (iGBRs; oscillations >30 Hz) elicited by familiar (meaningful) objects is well established in electroencephalogram (EEG) research. This frequency-specific change at distinct locations is thought to indicate the dynamic formation of local neuronal assemblies during the activation of cortical object representations. As analytically power increase is just a property of a single location, phase-synchrony was introduced to investigate the formation of large-scale networks between spatially distant brain sites. However, classical phase-synchrony reveals symmetric, pair-wise correlations and is not suited to uncover the directionality of interactions. Here, we investigated the neural mechanism of visual object processing by means of directional coupling analysis going beyond recording sites, but rather assessing the directionality of oscillatory interactions between brain areas directly. This study is the first to identify the directionality of oscillatory brain interactions in source space during human object recognition and suggests that familiar, but not unfamiliar, objects engage widespread reciprocal information flow. Directionality of cortical information-flow was calculated based upon an established Granger-Causality coupling-measure (partial-directed coherence; PDC) using autoregressive modeling. To enable comparison with previous coupling studies lacking directional information, phase-locking analysis was applied, using wavelet-based signal decompositions. Both, autoregressive modeling and wavelet analysis, revealed an augmentation of iGBRs during the presentation of familiar objects relative to unfamiliar controls, which was localized to inferior-temporal, superior-parietal and frontal brain areas by means of distributed source reconstruction. The multivariate analysis of PDC evaluated each possible direction of brain interaction and revealed widespread reciprocal information-transfer during familiar object processing. In contrast, unfamiliar objects entailed a sparse number of only unidirectional connections converging to parietal areas. Considering the directionality of brain interactions, the current results might indicate that successful activation of object representations is realized through reciprocal (feed-forward and feed-backward) information-transfer of oscillatory connections between distant, functionally specific brain areas.     

The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro

Since its outbreak in 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner. To gain deeper insight into mutation frequency and dynamics, we isolated ten ancestral strains of SARS-CoV-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-qPCR and whole genome sequencing. Along those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-CoV-2 in vitro. Our results identified a series of adaptive genetic changes, ranging from unique convergent substitutional mutations and hitherto undescribed insertions. The region coding for spike proved to be a mutational hotspot, evolving a number of mutational changes including the already known substitutions at positions S:484 and S:501. We discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-CoV-2 in the adaptation to cell culture. The combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-CoV-2 strains. The observed genetic changes of SARS-CoV-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants, along the path of increasing potency of the strain. Competition among a high number of quasi-species in the SARS-CoV-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change.     

Lower Statistical Support with Larger Data Sets: Insights from the Ochrophyta Radiation

It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid, and nucleus. Surprisingly while statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion (6,762 sites) and plastid (21,692 sites) trees, it decreases in the nuclear (209,105 sites) tree. Statistical support is not simply related to the data set size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that this ability for current phylogenetic methods is limited, because conflicting results were obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid data set provided higher statistical support for the ochrophyte radiation than the larger nucleus data set. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear data set. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of data sets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.     

Cloning of proline-specific endopeptidase gene from Flavobacterium meningosepticum: expression in Escherichia coli and purification of the heterologous protein

Proline-specific endopeptidase (PSE) (EC 3.4.21.26) from Flavobacterium meningosepticum was subjected to partial amino acid sequencing. According to the peptide sequences obtained, oligonucleotides were used to amplify a PSE-specific DNA fragment of 930 bp from F. meningosepticum genomic DNA, employing the polymerase chain reaction technique. This fragment served as a molecular probe to isolate the respective gene. DNA sequencing revealed that the PSE gene consists of 2118 bp coding for a 78,634 Da protein of 705 amino acids. The coding region was cloned in different expression vectors of Escherichia coli. Transformed E. coli cells overproduce an active prolyl endopeptidase of 75,000 relative molecular mass, which is delivered to the bacterial periplasmic space. Up to 1.6 units of active prolyl endopeptidase were obtained from 1 mg E. coli cells. Furthermore, the efficient purification of active prolyl endopeptidase from the periplasm of recombinant E. coli cells is described. Correspondence to: G. Reipen     

A high-throughput Arabidopsis reverse genetics system

A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymmetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from approximately 100000 transformed lines. A total of 85108 TAIL-PCR products from 52964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org.     

Low temperature tolerance and starvation ability of the oak processionary moth: implications in a context of increasing epidemics

• 1 We investigated how modifications in winter and spring temperature conditions may affect the survival of a spring‐hatching Lepidoptera, the oak processionary moth Thaumetopoea processionea.
• 2 Supercooling and chilling injury experiments indicate that eggs are especially cold hardy at the start of the winter period, although this ability is reduced later in the season. In the spring, young larvae are sufficiently cold hardy to ensure no direct mortality as a result of late frosts.
• 3 A comparison of phenological models shows that neonate larvae may await the unfolding of new oak leaves for relatively long periods (e.g. 1–30 days). Under both low (4°C after 5 days at 16°C) and high temperature experimental scenarios (constant 16°C), the majority of neonate larvae can survive starvation for more than 2 weeks.
• 4 Larvae may also suffer from food depletion once their development has been initiated (e.g. during cold springs) if the threshold temperature for feeding is not reached for several consecutive days, or in the case of late frosts affecting foliage availability. When temperature is reduced to 4°C, developing larvae become inactive and do not feed anymore; their starvation survival capability is reduced to approximately 2 weeks (cold spring hypothesis). At 16°C, developing larvae that are deprived of food can only survive for 10 days (late frost hypothesis).
• 5 We conclude that, in the oak processionary moth, neonate larvae are relatively well adapted to early hatching relative to budburst, ensuring them the highest foliage quality for development. In some years, however, phenological asynchrony or cold spring conditions may affect the persistence of populations at the limits of the species' range.

     

Modeling of mixing in 96-well microplates observed with fluorescence indicators

Mixing in 96-well microplates was studied using soluble pH indicators and a fluorescence pH sensor. Small amounts of alkali were added with the aid of a multichannel pipet, a piston pump, and a piezoelectric actuator. Mixing patterns were observed visually using a video camera. Addition of drops each of about 1 nL with the piezoelectric actuator resulted in umbrella and double-disklike shapes. Convective mixing was mainly observed in the upper part of the well, whereas the lower part was only mixed quickly when using the multichannel pipet and the piston pump with an addition volume of 5 microL or larger. Estimated mixing times were between a few seconds and several minutes. Mixing by liquid dispensing was much more effective than by shaking. A mixing model consisting of 21 elements could describe mixing dynamics observed by the dissolved fluorescence dye and by the optical immobilized pH sensor. This model can be applied for designing pH control in microplates or for design of kinetic experiments with liquid addition.     

Transport and metabolism of exogenously applied gibberellins to Malus domestica Borkh. cv. Jonagold

The radio-labeled gibberellins GA₁, GA₃,GA₄, and GA₇ were applied to intact developing applefruits (Malus domestica Borkh. cv. Jonagold) during theperiod when GAs are suggested to inhibit flower bud induction for the followingyear. Radioactivity from these compounds was found to be transported intoadjacent tissues as there are pedicels and bourses (4%). Application topedicels, after removal of the fruits, enhanced the transport into adjacentbourses up to 11%. The bud-carrying lateral bourse shoots contained onlyminor amounts of radioactivity on average 0.4% in both cases. Theseexport rates were identical, 1 or 5 days after application.After application of the corresponding deuterium-labeled GAs and analyses bymass spectrometry the specific metabolization of GA₁ toGA₁ 13-O-glucoside and of GA₃ to GA₃13-O-glucoside was demonstrated. Additional metabolites of GA₁ andGA₃ were not detected. After fruit application of GA₃ theratio of GA₃ to GA₃ 13-O-glucoside was found to be 1:2 inthe fruit. Pedicel application led to ratios of 1:4 and 1:5, respectively, inthe pedicel and in the adjacent bourse. After the application of GA₄and GA₇, neither glucosylation products nor other GA-like metabolitescould be identified.This is the first report of the metabolism of GAs to GA 13-O-glucosides indeveloping apple fruits. The possible function of the GAs as a signal in flowerbud formation for the following year is discussed.     

Induction of accessory cell function of human alveolar macrophages by inhalation of human natural interleukin-2

 Accessory function allows antigen-presenting cells to produce sufficient secondary signals for optimum T cell proliferation and interleukin-2 (IL-2) production. Alveolar macrophages are inferior accessory cells compared to monocytes (PBM). We report here that the accessory index (AI) of alveolar macrophages and PBM of patients with lung metastases of solid tumors treated with inhalations of human natural IL-2 (hnIL-2) increased following its administration (P<0.005). The accessory index was significantly elevated from baseline values after 2 weeks of inhalation of 300 000 IU hnIL-2/day (8.2±10.2 compared to 1.1±1; P<0.001). The inhalation of 150 000 IU also induced increases in the index (AI = 2.3±1.9), however, without reaching statistical significance. In addition at 300 000 IU IL-2/day a significant increase in the accessory index was observed for PBM (4±2.5; P<0.05). The indices of PBM and alveolar macrophages prior to inhalation showed a significant negative correlation with the age of the patients (r _s =  – 0.5; r _s =  – 0.8, respectively; P<0.03 for all comparisons). Our data demonstrate that the inhalational application of hnIL-2 enhances the accessory function of alveolar macrophages and, to lesser extent, the accessory index of PBM, indicating the occurrence of pharmacological immunostimulation. Received: 16 August 1995 / Accepted: 4 January 1996