Structure-based peptide ligand design for improved epidermal growth factor receptor targeted gene delivery.

The epidermal growth factor receptor EGFR allows targeted delivery of macromolecular drugs to tumors. Its ligand, epidermal growth factor, binds EGFR with high affinity but acts mitogenic. Non-mitogenic peptides are utilized as targeting ligands, like the dodecapeptide GE11, although its low binding affinity warrants improvement. We applied a two-step computational approach with database search and molecular docking to design GE11 variants with improved binding. Synthesized peptides underwent binding studies on immobilized EGFR using surface plasmon resonance. Conjugates of peptides coupled via heterobifunctional PEG linker to linear polyethylenimine (LPEI) were used for transfection studies on EGFR-overexpressing cells using reporter gene encoding plasmid DNA. Docking studies unraveled similarities between GE11 and the EGFR dimerization arm. By skipping non-overlapping amino acids, a less hydrophobic segment (YTPQNVI) was identified to be directly involved in EGFR binding. By replacing valine by tyrosine, a full-length version with proposed enhanced binding (GE11m3) was developed. While hydrophobic or hydrophilic segments and variations thereof exhibited low binding, GE11m3 exhibited 3-fold increase in binding compared to GE11, validating in silico predictions. In transfection studies, polyplexes with GE11m3 induced a significantly higher reporter gene expression when compared to GE11 polyplexes both on murine and human cancer cells overexpressing EGFR.

CXCR4 Is a Potential Target for Diagnostic PET/CT Imaging in Barrett's Dysplasia and Esophageal Adenocarcinoma.

Purpose: Barrett's esophagus represents an early stage in carcinogenesis leading to esophageal adenocarcinoma. Considerable evidence supports a major role for chronic inflammation and diverse chemokine pathways in the development of Barrett's esophagus and esophageal adenocarcinoma.Experimental Design: Here we utilized an IL1ß transgenic mouse model of Barrett's esophagus and esophageal adenocarcinoma and human patient imaging to analyze the importance of CXCR4-expressing cells during esophageal carcinogenesis.Results: IL1ß overexpression induces chronic esophageal inflammation and recapitulates the progression to Barrett's esophagus and esophageal adenocarcinoma. CXCR4 expression is increased in both epithelial and immune cells during disease progression in pL2-IL1ß mice and also elevated in esophageal adenocarcinoma patient biopsy samples. Specific recruitment of CXCR4-positive (CXCR4+) immune cells correlated with dysplasia progression, suggesting that this immune population may be a key contributor to esophageal carcinogenesis. Similarly, with progression to dysplasia, there were increased numbers of CXCR4+ columnar epithelial cells at the squamocolumnar junction (SCJ). These findings were supported by stronger CXCR4-related signal intensity in ex vivo fluorescence imaging and autoradiography with advanced dysplasia. Pilot CXCR4-directed PET/CT imaging studies in patients with esophageal cancer demonstrate the potential utility of CXCR4 imaging for the diagnosis and staging of esophageal cancer.Conclusion: In conclusion, the recruitment of CXCR4+ immune cells and expansion of CXCR4+ epithelial cells in esophageal dysplasia and cancer highlight the potential of CXCR4 as a biomarker and molecular target for diagnostic imaging of the tumor microenvironment in esophageal adenocarcinoma. Clin Cancer Res; 24(5); 1048-61. ©2017 AACR.

Choosing the optimal trigger point for analysis of movements after stroke based on magnetoencephalographic recordings.

The aim of this study was to select the optimal procedure for analysing motor fields (MF) and motor evoked fields (MEF) measured from brain injured patients. Behavioural pretests with patients have shown that most of them cannot stand measurements longer than 30 minutes and they also prefer to move the hand with rather short breaks between movements. Therefore, we were unable to measure the motor field (MF) optimally. Furthermore, we planned to use MEF to monitor cortical plasticity in a motor rehabilitation procedure. Classically, the MF analysis refers to rather long epochs around the movement onset (M-onset). We shortened the analysis epoch down to a range from 1000 milliseconds before until 500 milliseconds after M-onset to fulfil the needs of the patients. Additionally, we recorded the muscular activity (EMG) by surface electrodes on the extensor carpi ulnaris and flexor carpi ulnaris muscles. Magnetoencephalographic (MEG) data were recorded from 9 healthy subjects, who executed horizontally brisk extension and flexion in the right wrist. Significantly higher MF dipole strength was found in data based on EMG-onset than in M-onset based data. There was no difference in MEF I dipole strength between the two trigger latencies. In conclusion, we recommend averaging in respect to the EMG-onset for the analysis of both components MF as well as MEF.

caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.

The caBIG Compatibility Review System (CRS) is a web-based application to support compatibility reviews, which certify that software applications that pass the review meet a specific set of criteria that allow them to interoperate. The CRS contains workflows that support both semantic and syntactic reviews, which are performed by the caBIG Vocabularies and Common Data Elements (VCDE) and Architecture workspaces, respectively. The CRS increases the efficiency of compatibility reviews by reducing administrative overhead and it improves uniformity by ensuring that each review is conducted according to a standard process. The CRS provides metrics that allow the review team to evaluate the level of data element reuse in an application, a first step towards quantifying the extent of harmonization between applications. Finally, functionality is being added that will provide automated validation of checklist criteria, which will further simplify the review process.

'Candidatus Aquirestis calciphila' and 'Candidatus Haliscomenobacter calcifugiens', filamentous, planktonic bacteria inhabiting natural lakes.

Filamentous bacteria frequently occurring in the pelagic zone of natural freshwater lakes and ponds were previously identified as being related to Haliscomenobacter hydrossis based upon their 16S rRNA gene sequences. These bacteria exhibit a specific morphology characterized by the formation of straight, stick-like filaments of variable length (5 to >100 microm) and quite stable, but narrow, width (0.25 to 0.35 microm). Bacteria with these morphological characteristics form a monophyletic but broad phylogenetic group with a maximal divergence of 16S rRNA gene sequences of 12.0 %. This monophyletic group consists of at least three monophyletic subclusters. H. hydrossis is affiliated to one of these subclusters and represents the sole recognized species affiliated to the broad monophyletic group. 'Candidatus Haliscomenobacter calcifugiens' and 'Candidatus Aquirestis calciphila' are uncultured representatives of the other two subclusters and have 16S rRNA gene sequence dissimilarities of 5.4 % and 8.2 %, respectively, with the type strain of H. hydrossis. 'Candidatus H. calcifugiens' and 'Candidatus A. calciphila' have a 16S rRNA gene sequence dissimilarity of 8.5 %. These large ribosomal divergences justify the classification of these environmentally important bacteria as a novel species and a new genus, respectively. Intensive attempts to cultivate these filamentous bacteria have resulted in the establishment of mixed cultures, however, attempts to establish pure cultures have failed.

Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China.

The influence of altitude and salinity on bacterioplankton community composition (BCC) in 16 high-mountain lakes located at altitudes of 2,817 to 5,134 m on the Eastern Qinghai-Xizang (Tibetan) Plateau, China, spanning a salinity gradient from 0.02% (freshwater) to 22.3% (hypersaline), was investigated. Three different methods, fluorescent in situ hybridization, denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing, and reverse line blot hybridization (RLB) with probes targeting 17 freshwater bacterial groups, were used for analysis of BCC. Furthermore, the salt tolerances of 47 strains affiliated with groups detected in or isolated from the Tibetan habitats were investigated. Altitude was not found to influence BCC significantly within the investigated range. Several groups of typical freshwater bacteria, e.g., the ACK-M1 cluster and the Polynucleobacter group, were detected in habitats located above 4,400 m. Salinity was found to be the dominating environmental factor controlling BCC in the investigated lakes, resulting in only small overlaps in the BCCs of freshwater and hypersaline lakes. The relative abundances of different classes of Proteobacteria showed a sharp succession along the salinity gradient. Both DGGE and RLB demonstrated that a few freshwater bacterial groups, e.g., GKS98 and LD2, appeared over wide salinity ranges. Six freshwater isolates affiliated with the GKS98 cluster grew in ecophysiological experiments at maximum salinities of 0.3% to 0.7% (oligosaline), while this group was detected in habitats with salinities up to 6.7% (hypersaline). This observation indicated ecologically significant differences in ecophysiological adaptations among members of this narrow phylogenetic group and suggested ecological significance of microdiversity.

Recurrent seasonal variations in abundance and composition of filamentous SOL cluster bacteria (Saprospiraceae, Bacteroidetes) in oligomesotrophic Lake Mondsee (Austria).

The spatial and temporal variation of SOL cluster bacteria was assessed in oligomesotrophic Lake Mondsee and adjacent lakes by fluorescence in situ hybridization over two annual cycles. The filamentous SOL bacteria were present in Lake Mondsee throughout the study period, and the seasonal dynamics of the SOL community were remarkably similar with respect to both abundance and composition in the two consecutive years. Only two of the three SOL subclusters were detected in Lake Mondsee and four connected lakes. These two populations significantly differed in size distribution and demonstrated pronounced but recurrent differences in seasonality and length of period of appearance in Lake Mondsee. Extensive sampling of the lakes in September 2003 revealed low horizontal variation in the composition of the SOL community within Lake Mondsee but marked variations with depth. Between connected habitats pronounced differences in the composition and abundance of the SOL community were detected. The interaction of SOL bacteria with bacterivorous protists, mesozooplankton, and phytoplankton was investigated in order to reveal variables controlling the structure and dynamics of SOL communities. No strong indication for a bottom-up influence of phytoplankton was found, while the estimated community grazing rates of mesozooplankton on SOL bacteria indicated a top-down control of SOL abundance during mesozooplankton peaks in spring and early autumn. Furthermore, species-specific differences in grazing of mesozooplankton on SOL bacteria were observed. In general, the overall composition of SOL communities was controlled by abiotic factors (water chemistry), while their dynamics seemed to be controlled by abiotic and biotic interactions.

Generation and optimization of human antagonistic antibodies against TIMP-1 as potential therapeutic agents in fibrotic diseases.

Impaired matrix metalloproteinase 1 (MMP-1) function, as result of the expression of increased levels of tissue inhibitor of metalloproteinase 1 (TIMP-1), plays an important role in the pathopysiolgical mechanism of fibrosis. In a recently performed clinically relevant rat animal model of established liver fibrosis, it could be shown, that blocking the interaction between the metalloproteinase and its inhibitor has beneficial effects in vivo. The rat TIMP-1 specific antagonistic antibody used in this study was derived from a human combinatorial antibody library (HuCAL) and blocks the interaction between rat TIMP-1 and MMP-13, the rat homologue of human MMP-1. We here describe the utilization of the same antibody source to generate fully human antibodies against human TIMP-1 which could be potential candidates for a therapy of fibrosis in man. In order to develop a highly potent antagonist of TIMP-1 action, antibodies isolated from the library were subjected to a number of different in vitro affinity maturation strategies. By these means, affinity and potency were improved by a factor of 87 and 65 fold, respectively, resulting in a valuable human therapeutic antibody candidate with a monovalent affinity of 150 pM and a potency for in vitro inhibition of TIMP-1/MMP-1 interaction of 200 pM.

Ecological differentiation within a cosmopolitan group of planktonic freshwater bacteria (SOL cluster, Saprospiraceae, Bacteroidetes).

Members of the monophyletic SOL cluster are large filamentous bacteria inhabiting the pelagic zone of many freshwater habitats. The abundances of SOL bacteria and compositions of SOL communities in samples from 115 freshwater ecosystems around the globe were determined by fluorescence in situ hybridization with cluster- and subcluster-specific oligonucleotide probes. The vast majority (73%) of sampled ecosystems harbored SOL bacteria, and all three previously described SOL subclusters (LD2, HAL, and GKS2-217) were detected. The morphometric and chemicophysical parameters and trophic statuses of ecosystems were related to the occurrence and subcluster-specific composition of SOL bacteria by multivariate statistical methods. SOL bacteria did not occur in acidic lakes (pH < 6), and their abundance was negatively related to high trophy and pH. The subcluster-specific variation in the compositions of SOL communities could be related to the pH, electrical conductivity, altitude, and trophic status of ecosystems. All three known SOL subclusters differed in respect to their tolerated ranges of pH and conductivity. Complete niche separation was observed between the vicarious subclusters GKS2-217 and LD2; the former occurred in soft-water lakes, whereas the latter was found in a broad range of hard-water habitats. The third subgroup (HAL) showed a wide environmental tolerance and was usually found sympatrically with the LD2 or GKS2-217 subcluster. Ecological differentiation of SOL bacteria at the subcluster level was most probably driven by differential adaptation to water chemistry. The distribution of the two vicarious taxa seems to be predominantly controlled by the geological backgrounds of the catchment areas of the habitats.

Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of beta-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir.

We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Rímov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 microm), bacteria and heterotrophic nanoflagellates (<5 microm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of beta-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory.

Diversity and phylogenetic affiliations of morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum of freshwater habitats.

Filamentous bacteria with a conspicuous morphology were found in the majority of the bacterioplankton samples from a variety of freshwater habitats that were studied. These heterotrophic filaments typically account for < 1 to 11% of the total number of bacteria. The biovolume of this morphotype can exceed 40% of the biovolume for all bacteria. Surprisingly, we found hardly any data on these morphologically conspicuous filaments in the literature. Mixed cultures containing these filamentous bacteria were established by cultivation and isolation experiments with samples from different freshwater lakes. Nearly full-length 16S rRNA gene sequences were obtained from several mixed cultures and environmental samples from habitats in Europe, Africa, China, Australia, and New Zealand. Phylogenetic analysis of the sequences showed that three groups form a single monophyletic cluster, the SOL cluster, in the family Saprospiraceae. We developed a set of six nested probes for fluorescence in situ hybridization. Of the six probes, one probe was specific for Haliscomenobacter hydrossis, three probes were specific for the three subclusters (each probe was specific for one subcluster), one probe was specific for the entire SOL cluster, and another probe targeted almost the entire Saprospiraceae family. Specific hybridization of environmental samples and enrichments showed that the members of the three subclusters exhibited the same filamentous morphology. So far, using the subcluster-specific probes, we have not been able to detect any bacteria with a differing morphology. We conclude that the SOL cluster bacteria are an integral part of bacterioplankton in many freshwater habitats. They potentially account for a large fraction of the total bacterial biomass but have been underrepresented in molecular diversity studies so far.

Antifibrotic effects of a tissue inhibitor of metalloproteinase-1 antibody on established liver fibrosis in rats.

Liver fibrosis is characterized by increased synthesis, and decreased degradation, of extracellular matrix (ECM) within the injured tissue. Decreased ECM degradation results, in part, from increased expression of tissue inhibitor of metalloproteinase-1 (TIMP-1), which blocks matrix metalloproteinase (MMP) activity. TIMP-1 is also involved in promoting survival of activated hepatic stellate cells (HSCs), a major source of ECM. This study examined the effects of blocking TIMP-1 activity in a clinically relevant model of established liver fibrosis. Rats were treated with carbon tetrachloride (CCl(4)), or olive oil control, for 6 weeks; 24 days into the treatment, the rats were administered a neutralizing anti-TIMP-1 antibody derived from a fully human combinatorial antibody library (HuCAL), PBS, or an isotype control antibody. Livers from CCl(4)-treated rats exhibited substantial damage, including bridging fibrosis, inflammation, and extensive expression of smooth muscle alpha-actin (alpha-SMA). Compared to controls, rats administered anti-TIMP-1 showed a reduction in collagen accumulation by histological examination and hydroxyproline content. Administration of anti-TIMP-1 resulted in a marked decrease in alpha-SMA staining. Zymography analysis showed antibody treatment decreased the activity of MMP-2. In conclusion, administration of a TIMP-1 antibody attenuated CCl(4)-induced liver fibrosis and decreased HSC activation and MMP-2 activity.

Musical motor feedback (MMF) in walking hemiparetic stroke patients: randomized trials of gait improvement.

OBJECTIVE: To demonstrate the effect of rhythmical auditory stimulation in a musical context for gait therapy in hemiparetic stroke patients, when the stimulation is played back measure by measure initiated by the patient's heel-strikes (musical motor feedback). Does this type of musical feedback improve walking more than a less specific gait therapy? DESIGN: The randomized controlled trial considered 23 registered stroke patients. Two groups were created by randomization: the control group received 15 sessions of conventional gait therapy and the test group received 15 therapy sessions with musical motor feedback. SETTING: Inpatient rehabilitation hospital. SUBJECTS: Median post-stroke interval was 44 days and the patients were able to walk without technical aids with a speed of approximately 0.71 m/s. MAIN OUTCOME MEASURES: Gait velocity, step duration, gait symmetry, stride length and foot rollover path length (heel-on-toe-off distance). RESULT: The test group showed more mean improvement than the control group: stride length increased by 18% versus 0%, symmetry deviation decreased by 58% versus 20%, walking speed increased by 27% versus 4% and rollover path length increased by 28% versus 11%. CONCLUSION: Musical motor feedback improves the stroke patient's walk in selected parameters more than conventional gait therapy. A fixed memory in the patient's mind about the song and its timing may stimulate the improvement of gait even without the presence of an external pacemaker.

Dissociation of human and computer voices in the brain: evidence for a preattentive gestalt-like perception.

We investigated the early ("preattentive") cortical processing of voice information, using the so-called "mismatch response". This brain potential allows inferences to be made about the sensory short-term store. Most importantly, the mismatch potential also provides information about the organization of long-term memory traces in the auditory system. Such traces have reliably been reported for phonemes. However, it is unclear whether they also exist for human voice information. To explore this issue, 10 healthy subjects were presented with a single word stimulus uttered by voices of different prototypicality (natural, manipulated, synthetic) in a mismatch experiment (stimulus duration 380 msec, onset-to-onset interval 900 msec). The event-related magnetic fields were recorded by a 148-channel whole-head magnetometer and a source current density modeling of the magnetic field data was performed using a minimum-norm estimate. Each deviating voice signal in a series of standard-voice stimuli evoked a mismatch response that was localized in temporal brain regions bilaterally. Increased mismatch related magnetic flux was observed in response to decreased prototypicality of a presented voice signal, but did not correspond to the acoustic similarity of standard voice and deviant voices. We, therefore, conclude that the mismatch activation predominantly reflects the ecological validity of the voice signals. We further demonstrate that the findings cannot be explained by mere acoustic feature processing, but rather point towards a holistic mapping of the incoming voice signal onto long-term representations in the auditory memory.

Isolation of novel ultramicrobacteria classified as actinobacteria from five freshwater habitats in Europe and Asia.

We describe the first freshwater members of the class Actinobacteria that have been isolated. Nine ultramicro-size (<0.1 microm(3)) strains were isolated from five freshwater habitats in Europe and Asia. These habitats represent a broad spectrum of ecosystems, ranging from deep oligotrophic lakes to shallow hypertrophic lakes. Even when the isolated strains were grown in very rich media, the cell size was <0.1 microm(3) and was indistinguishable from the cell sizes of bacteria belonging to the smaller size classes of natural lake bacterioplankton. Hybridization of the isolates with oligonucleotide probes and phylogenetic analysis of the 16S rRNA gene sequences of the isolated strains revealed that they are affiliated with the class Actinobacteria and the family Microbacteriaceae. The previously described species with the highest levels of sequence similarity are Clavibacter michiganensis and Rathayibacter tritici, two phytopathogens of terrestrial plants. The 16S rRNA gene sequences of the nine isolates examined are more closely related to cloned sequences from uncultured freshwater bacteria than to the sequences of any previously isolated bacteria. The nine ultramicrobacteria isolated form, together with several uncultured bacteria, a diverse phylogenetic cluster (Luna cluster) consisting exclusively of freshwater bacteria. Isolates obtained from lakes that are ecologically different and geographically separated by great distances possess identical 16S rRNA gene sequences but have clearly different ecophysiological and phenotypic traits. Predator-prey experiments demonstrated that at least one of the ultramicro-size isolates is protected against predation by the bacterivorous nanoflagellate Ochromonas sp. strain DS.

Early parallel processing of auditory word and voice information.

The present study investigates the relationship of linguistic (phonetic) and extralinguistic (voice) information in preattentive auditory processing. We provide neurophysiological data, which show for the first time that both kinds of information are processed in parallel at an early preattentive stage. In order to establish the temporal and spatial organization of the underlying neuronal processes, we studied the conjunction of voice and word deviations in a mismatch negativity experiment, whereby the listener's brain responses were collected using magnetoencephalography. The stimuli consisted of single spoken words, whereby the deviants manifested a change of the word, of the voice, or both word and voice simultaneously (combined). First, we identified the N100m (overlain by mismatch field, MMF) and localized its generators, analyzing N100 m/MMF latency, dipole localization, and dipole strength. While the responses evoked by deviant stimuli were more anterior than the standard, localization differences between the deviants could not be shown. The dipole strength was larger for deviants than the standard stimulus, but again, no differences between the deviants could be established. There was no difference in the hemispheric lateralization of the responses. However, a difference between the deviants was observed in the latencies. The N100 m/MMF revealed a significantly shorter and less variant latency for the combined stimulus compared to all other experimental conditions. The data suggest an integral parallel processing model, which describes the early extraction of phonetic and voice information from the speech signal as parallel and contingent processes.