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Chatterjee, A.

Publications and source records attributed to Chatterjee, A..

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Galectin-1 promotes the invasion of bladder cancer urothelia through their matrix milieu

The progression of carcinoma of the urinary bladder involves migration of cancer epithelia through their surrounding tissue matrix microenvironment. This was experimentally confirmed when a gender- and grade-diverse set of bladder cancer cell lines were cultured in pathomimetic three-dimensional laminin-rich environments. The high-grade cells, particularly female, formed multicellular invasive morphologies in 3D. In comparison, low- and intermediate-grade counterparts showed growth-restricted phenotypes. A proteomic approach combining mass spectrometry and bioinformatics analysis identified the estrogen-driven lactose-binding lectin Galectin-1 (GAL-1) as a putative candidate that could drive this invasion. Expression of LGALS1, the gene encoding GAL-1 showed an association with tumor grade progression in bladder cell lines. Immunohisto- and cyto-chemical experiments suggested greater extracellular levels of GAL-1 in 3D cultures of high-grade bladder cells and cancer tissues. High levels of GAL-1 associated with increased proliferation- and adhesion- of bladder cancer cells when grown on laminin-rich matrices. Pharmacological inhibition and Gal-1 knockdown in high-grade female cells decreased their adhesion to, and viability on, laminin-rich substrata. Higher GAL-1 also correlated with reduced E-cadherin and increased N-cadherin levels in consonance with a mesenchymal-like phenotype that we observed in 3D culture. The inhibition of GAL-1 reversed the stellate invasive phenotype to a more growth-restricted one in high-grade cells embedded within both basement-membrane-like and stromal collagenous matrix scaffolds. Finally, inhibition of GAL-1 specifically altered cell surface sialic acids, suggesting the mechanism by which the levels of GAL-1 may underlie the aggression and poor prognosis of invasive bladder cancer, especially in women.

cancer biology

Everyday taxi drivers: Do better navigators have larger hippocampi?

Work with non-human animals and human navigation experts (London taxi drivers) suggests that the size of the hippocampus, particularly the right posterior hippocampus in humans, relates to navigation expertise. Similar observations, sometimes implicating other sections of the hippocampus, have been made for aging populations and for people with neurodegenerative diseases that affect the hippocampus. These data support the hypothesis that hippocampal volume relates to navigation ability. However, the support for this hypothesis is mixed in healthy, young adults, who range widely in their navigation ability. Here, we administered a naturalistic navigation task that measures cognitive map accuracy to a sample of 90 healthy, young adults who also had MRI scans. Using a sequential analysis design with a registered analysis plan, we did not find that navigation ability related to hippocampal volume (total, right only, right posterior only). We conclude that navigation ability in a typical population does not correlate with variations in hippocampal size, and consider possible explanations for this null result.

neuroscience

Design of a de novo aggregating antimicrobial peptide and bacterial conjugation delivery system

Traditional antibiotics are reaching obsolescence as a consequence of antibiotic resistance; therefore novel antibiotic approaches are needed. A recent non-traditional approach involves formation of protein aggregates as antimicrobials to disrupt bacterial homeostasis. Previous work on protein aggregates has focused on genome mining for aggregation-prone sequences in bacterial genomes rather than on rational design of aggregating antimicrobial peptides. Here, we use a synthetic biology approach to design an artificial gene encoding the first de novo aggregating antimicrobial peptide. This artificial gene, opaL (overexpressed protein aggregator Lipophilic), disrupts bacterial homeostasis by expressing extremely hydrophobic peptides. When this hydrophobic sequence is disrupted by acidic residues, consequent aggregation and antimicrobial effect decreases. Further, to deliver this artificial gene, we developed a probiotic approach using RK2, a broad host range conjugative plasmid, to transfer opaL from donor to recipient bacteria. We utilize RK2 to mobilize a shuttle plasmid carrying the opaL gene by adding the RK2 origin of transfer. We show that opaL is non-toxic to the donor, allowing for maintenance and transfer since its expression is under control of a promoter with a recipient-specific T7 RNA polymerase. Upon mating of donor and recipient Escherichia coli, we observe selective growth repression in T7 polymerase expressing recipients. This technique could be used to target desired pathogens by selecting pathogen-specific promoters to control opaL expression. This system provides a basis for the design and delivery of novel antimicrobial peptides.\n\nImportanceThe growing threat of antibiotic resistance necessitates new treatment options for bacterial infections that are recalcitrant to traditional antimicrobials. Existing methods usually involve small-molecule compounds which interfere with essential processes in bacterial cells. By contrast, protein aggregates operate by causing widespread disruption of bacterial homeostasis and may provide a new method for combating infections. We used rational design to create and test an aggregating de novo antimicrobial peptide, OpaL. In addition, we employed bacterial conjugation to deliver the opaL gene from donor bacteria to recipient bacteria while using a strain-specific promoter to ensure that OpaL was only expressed in targeted recipients. To the best of our knowledge, this represents the first design for a de novo peptide with aggregation-mediated antimicrobial activity. We envision that OpaLs design parameters could be used in developing a new class of antimicrobial peptides to help treat antibiotic resistant infections.

microbiology

UNC-16/JIP3 and UNC-76/FEZ1 limit the density of mitochondria in C. elegans neurons by maintaining the balance of anterograde and retrograde mitochondrial transport

We investigate the role of axonal transport in regulating neuronal mitochondrial density. We show that the density of mitochondria in the touch receptor neuron (TRN) of adult Caenorhabditis elegans is constant. Mitochondrial density and transport are controlled both by the Kinesin heavy chain and the Dynein-Dynactin complex. However, unlike in other models, the presence of mitochondria in C. elegans TRNs depends on Kinesin light chain as well. Mutants in the three C. elegans miro genes do not alter mitochondrial density in the TRNs. Mutants in the Kinesin-1 associated proteins, UNC-16/JIP3 and UNC-76/FEZ1, show increased mitochondrial density and also have elevated levels of both the Kinesin Heavy and Light Chains in neurons. Genetic analyses suggest that, the increased mitochondrial density at the distal end of the neuronal process in unc-16 and unc-76 depends partly on Dynein. We observe a net anterograde bias in the ratio of anterograde to retrograde mitochondrial flux in the neuronal processes of unc-16 and unc-76, likely due to both increased Kinesin-1 and decreased Dynein in the neuronal processes. Our study shows that UNC-16 and UNC-76 indirectly limit mitochondrial density in the neuronal process maintaining a balance in anterograde and retrograde mitochondrial axonal transport.

genetics

Making honey bees lie: experimental dissociation of flight experience and dance communication.

Honey bees use their dance to communicate flight distance and direction of a food source to their nest mates in the hive. How bees transpose flight information to generate a corresponding walking (dance) behavior is still unknown. We now present a detailed study of the changes in dance duration of individual bees after shifting feeder distance. Our experiments indicated that most bees needed two or more foraging trips to the new position before showing an updated dance duration. In addition, only a few bees significantly changed dance duration immediately, whereas most bees first produced intermediary durations. Double shift experiments showed that under certain conditions bees do not update dance duration but continued to perform dance duration for the previously visited feeder position. We propose that generation of dance information involves two memory contents one for newly acquired and one for previously stored distance information.\n\nOne Sentence SummaryGeneration of dance information is temporally separated from immediate flight experience and involves two different memory contents.

animal behavior and cognition

Behavioral and neural representations of spatial directions across words, schemas, and images

Modern spatial navigation requires fluency with multiple representational formats, including visual scenes, signs, and words. These formats convey different information. Visual scenes are rich and specific, but contain extraneous details. Arrows, as an example of signs, are schematic representations in which the extraneous details are eliminated, but analog spatial properties are preserved. Words eliminate all spatial information and convey spatial directions in a purely abstract form. How does the human brain compute spatial directions within and across these formats? To investigate this question, we conducted two experiments on men and women: a behavioral study that was preregistered, and a neuroimaging study using multivoxel pattern analysis of fMRI data to uncover similarities and differences among representational formats. Participants in the behavioral study viewed spatial directions presented as images, schemas, or words (e.g., \"left\"), and responded to each trial, indicating whether the spatial direction was the same or different as the one viewed previously. They responded more quickly to schemas and words than images, despite the visual complexity of stimuli being matched. Participants in the fMRI study performed the same task, but responded only to occasional catch trials. Spatial directions in images were decodable in the intraparietal sulcus (IPS) bilaterally, but were not in schemas and words. Spatial directions were also decodable between all three formats. These results suggest that IPS plays a role in calculating spatial directions in visual scenes, but this neural circuitry may be bypassed when the spatial directions are presented as schemas or words.\n\nSignificance StatementHuman navigators encounter spatial directions in various formats: words (\"turn left\"), schematic signs (an arrow showing a left turn), and visual scenes (a road turning left). The brain must transform these spatial directions into a plan for action. Here, we investigate similarities and differences between neural representations of these formats. We found that bilateral intraparietal sulci represents spatial directions in visual scenes and across the three formats. We also found that participants respond quickest to schemas, then words, then images, suggesting that spatial directions in abstract formats are easier to interpret than concrete formats. These results support a model of spatial direction interpretation in which spatial directions are either computed for real world action, or computed for efficient visual comparison.

neuroscience

Phenome-wide association studies (PheWAS) across large "real-world data" population cohorts support drug target validation

Phenome-wide association studies (PheWAS), which assess whether a genetic variant is associated with multiple phenotypes across a phenotypic spectrum, have been proposed as a possible aid to drug development through elucidating mechanisms of action, identifying alternative indications, or predicting adverse drug events (ADEs). Here, we evaluate whether PheWAS can inform target validation during drug development. We selected 25 single nucleotide polymorphisms (SNPs) linked through genome-wide association studies (GWAS) to 19 candidate drug targets for common disease therapeutic indications. We independently interrogated these SNPs through PheWAS in four large \"real-world data\" cohorts (23andMe, UK Biobank, FINRISK, CHOP) for association with a total of 1,892 binary endpoints. We then conducted meta-analyses for 145 harmonized disease endpoints in up to 697,815 individuals and joined results with summary statistics from 57 published GWAS. Our analyses replicate 70% of known GWAS associations and identify 10 novel associations with study-wide significance after multiple test correction (P<1.8x10-6; out of 72 novel associations with FDR<0.1). By leveraging directionality and point estimate of the effect sizes, we describe new associations that may predict ADEs, e.g., acne, high cholesterol, gout and gallstones for rs738409 (p.I148M) in PNPLA3; or asthma for rs1990760 (p.T946A) in IFIH1. We further propose how quantitative estimates of genetic safety/efficacy profiles can be used to help prioritize candidate targets for a specific indication. Our results demonstrate PheWAS as a powerful addition to the toolkit for drug discovery.\n\nOne Sentence SummaryMatching genetics with phenotypes in 800,000 individuals predicts efficacy and on-target safety of future drugs.

genetics

Feel the way with a vibrotactile compass: Does a navigational aid aid navigation?

Knowing where north is provides a navigator with invaluable information for learning and recalling a space, particularly in places with limited navigational cues, like complex indoor environments. Although north is effectively used by orienteers, pilots, and military personnel, very little is known about whether non-expert populations can or will use north to create an accurate representation of an indoor space. In the current study, we taught people two non-overlapping routes through a complex indoor environment, with which they were not familiar - a university hospital with few windows and several turns. Along one route, they wore a vibrotactile compass on their arm, which vibrated continuously indicating the direction of north. Along the other route, they were only told where north was at the start of the route. At the beginning, the end, and back at the beginning of each route, participants pointed to well-known landmarks in the surrounding city and campus (external landmarks), and newly-learned landmarks in the hospital (internal landmarks). We found improved performance with the compass only for external landmarks, driven by peoples use of the availability of north to orient these judgments. No such improved orientation occurred for the internal landmarks. These findings reveal the utility of vibrotactile compasses for learning new indoor spaces. We speculate that such cues help users map new spaces onto familiar spaces or to familiar reference frames.Keywords: Spatial navigation; vibrotactile compass; reference frames; spatial memory; pointing; real world navigation.\n\nGetting lost in complex indoor spaces, like hospitals, airports, or subways, can be dangerous, distressing, and costly. Unlike outdoor spaces, which typically offer long sightlines and distal landmarks, indoor spaces are often confined, undifferentiated, and labyrinthine. Individual building layouts can be hard to learn if knowledge about direction with respect to the larger world is not easily attained. Confusing layouts, signs, and an inability to see outdoor landmarks compound these problems. Even in places with adequate signs or sight of outdoor landmarks, successful navigation by blind people and people with visual impairments is a substantial problem (Schinazi, 2008; Schinazi, Thrash, & Chebat, 2016). In the current study, we investigate whether providing non-visual directional information aids sighted people in learning an unfamiliar, complex indoor space. Specifically, we tested how people use a commercially-available vibrotactile compass, which vibrates in the direction of north. Unlike visual compasses, people with visual impairments can use vibrotactile compasses. A non-visual aid might also limit divided attention, which complicates the use of visual aids (Gardony, Brunye, & Taylor, 2015).\n\nWe tested two competing hypotheses in the current study. These hypotheses stem from a multifarious theoretical framework of navigational ability (Wolbers & Hegarty, 2010). 1. General: People would have access to more spatial information, and thus improve generally. In this case, providing a specific spatial cue decreases the error in the sensory signals, increasing the fidelity of the resulting spatial representations. We would expect improved performance across all aspects of navigation behavior. 2. Specific: People would have access to a specific spatial cue, and thus improve on tasks for which that cue is immediately helpful. In this case, providing a specific spatial cue only improves access to specific information, but in a way that does not create a more accurate general spatial representation. We would expect improved performance only on aspects of navigation behavior that knowledge of the cue is directly relevant. Addressing these questions offers insights into how spatial information is acquired in general, and provides insight into how vibrotactile compasses might aid blind or visually impaired navigators.\n\nWhy might people get lost in complex indoor spaces? One reason is that place-based strategies used by humans to navigate are thwarted by indoor spaces. Research on humans and rats reveals two neural systems, which undergird two navigational strategies (Hartley, Maguire,Spiers, & Burgess, 2003; Marchette, Bakker, & Shelton, 2011; McDonald & White, 1994;Morris, Garrud, Rawlins, & OKeefe, 1982; Munn, 1950; Packard & McGaugh, 1996; Restle, 1957; Tolman, Ritchie, & Kalish, 1946). First, a place-based strategy, implemented by the hippocampus, represents space as a cognitive map. A cognitive map is a flexible spatial representation, which affords the opportunity to infer novel shortcuts. Second, a response strategy, implemented by the caudate nucleus, applies a stimulus-response approach to navigation whereby choice points are identified, and responses are recalled (e.g., turn left at the bank, then right at the big tree). The response strategy is relatively inflexible, and generates associations between scenes and actions. In indoor environments, cues that support a place strategy, like distal landmarks and visual discriminability (Restle, 1957) are absent. Instead, place strategies rely on a process of path integration - tracking ones movement away from a starting location by attending to translations and rotations. Unfortunately, unlike rodents, people are poor path integrators (Foo, Duchon, Warren, & Tarr, 2007; Loomis et al., 1993). Thus, in indoor spaces, if people are more likely to adhere to response-based strategies, they are likely to gain less spatial knowledge about the overall environment.\n\nA second reason people easily get lost in complex indoor spaces arises from research on reference frames. A large body of evidence (Diwadkar & McNamara, 1997; McNamara, Rump, & Werner, 2003; Meilinger, Riecke, & Bulthoff, 2014; Meilinger, Frankenstein, Watanabe, Bulthoff, & Holscher, 2015; Mou & McNamara, 2002; Mou, McNamara, & Zhang, 2013; Mou & Wang, 2015; Roskos-Ewoldsen, McNamara, Shelton, & Carr, 1998; Shelton & McNamara,2004) supports the idea that spatial knowledge is stored in a preferred reference frame. A reference frame is a spatial representation in which objects or other representations of space are contained, or with respect to which they are ordered, oriented, located, or thought to move; a preferred reference frame is an orientation in which a spatial layout is most easily recalled. A reference frame is considered global if it is common across multiple areas of space (e.g., global north). In familiar, large-scale (i.e., city-sized) spaces, reference frames can be aligned with north (Frankenstein, Mohler, Bulthoff, & Meilinger, 2011), or a salient organizing feature (like a street through a campus; Marchette, Yerramsetti, Burns, & Shelton, 2011; Yerramsetti, Marchette, & Shelton, 2013). Indoor environments, however, provide less access to global reference frames. In the absence of global cues (like distal landmarks), people are likely to organize space into several local reference frames, instead of one global reference frame (Meilinger et al., 2014). In the extreme, using local reference frames means each segment of a route is disconnected from the last, and results in a 1-dimensional representation of space (i.e., an ordered sequence of places, with no 2-dimensional spatial relations specified; Ishikawa & Montello, 2006). Being able to integrate across areas of a learned route to take novel shortcuts, for example, requires some spatial knowledge about how to join local reference frames to each other to form a global reference frame - a difficult and demanding cognitive process (Weisberg & Newcombe, 2016; Weisberg, Schinazi, Newcombe, Shipley, & Epstein, 2014).\n\nIf people have direct sensory access to a global spatial direction, like a cardinal direction, they might map an unfamiliar indoor space onto the larger external environment, and construct a more accurate spatial representation of this indoor space. In this way, place-based strategies and global reference frames become more useful in an unfamiliar indoor space. Recent work has begun to characterize the use of vibrotactile compasses in particular. Konig and colleagues (Karcher, Fenzlaff, Hartmann, Nagel, & Konig, 2012; Kaspar, Konig, Schwandt, & Konig, 2014; Konig et al., 2016) developed a feelSpace belt, which provides tactile information about magnetic north. Their work illustrates that, with extensive training (seven weeks), the vibrotactile compass can improve basic homing tasks in sighted individuals (Konig et al., 2016).However, it is unknown how such directional information is incorporated into spatial representations, particularly in complex indoor spaces. Moreover, we were interested in whether this directional information could be incorporated and used to learn a new environment with only rudimentary training in the use of the device.

animal behavior and cognition

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near point of care.\n\nWe demonstrate a low-cost DNA extraction method for TB WGS direct from patient samples. We initially evaluated the method using the Illumina MiSeq sequencer (40 smear-positive respiratory samples, obtained after routine clinical testing, and 27 matched liquid cultures). M. tuberculosis was identified in all 39 samples from which DNA was successfully extracted. Sufficient data for antibiotic susceptibility prediction was obtained from 24 (62%) samples; all results were concordant with reference laboratory phenotypes. Phylogenetic placement was concordant between direct and cultured samples. Using an Illumina MiSeq/MiniSeq the workflow from patient sample to results can be completed in 44/16 hours at a cost of {pound}96/{pound}198 per sample.\n\nWe then employed a non-specific PCR-based library preparation method for sequencing on an Oxford Nanopore Technologies MinION sequencer. We applied this to cultured Mycobacterium bovis BCG strain (BCG), and to combined culture-negative sputum DNA and BCG DNA. For the latest flowcell, the estimated turnaround time from patient to identification of BCG was 6 hours, with full susceptibility and surveillance results 2 hours later. Antibiotic susceptibility predictions were fully concordant. A critical advantage of the MinION is the ability to continue sequencing until sufficient coverage is obtained, providing a potential solution to the problem of variable amounts of M. tuberculosis in direct samples.

microbiology