Biology subjects

Singh, I.

Publications and source records attributed to Singh, I..

5 recordsLinked to original sources

bioRxiv2018

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in analog hosts

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation because of host responses and cellular damage. The native upper respiratory tract (URT) microbiome likely plays a role, yet the effects of influenza infection on the URT microbiome are largely unknown. We performed a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes had stable \"heathy ecostate\" communities both within and between individuals. In contrast, infected patients and ferrets exhibited large changes in bacterial community composition over time and between individuals. The \"unhealthy\" ecostates of infected individuals progressed towards the \"healthy ecostate\" over time, coinciding with viral clearance and recovery. Blooms of Pseudomonas were a statistically associated constant in the disturbed microbiomes of infected individuals. The dynamic and resilient nature of the microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.\n\nOne Sentence SummaryDynamics of the upper respiratory tract microbiome during influenza A virus infection

microbiology↗

bioRxiv2017

Scanning along a compressed timeline of the future

Several authors have suggested a deep symmetry between the psychological processes that underlie our ability to remember the past and make predictions about the future. The judgment of recency (JOR) task measures temporal order judgments for the past by presenting pairs of probe stimuli; participants choose the probe that was presented more recently. We performed a short-term relative JOR task and introduced a novel judgment of imminence (JOI) task to study temporal order judgments for the future. In the JOR task, participants were presented with a sequence of stimuli and asked to choose which of two probe stimuli was presented closer to the present. In the JOI task, participants were trained on a probabilistic sequence. After training, the sequence was interrupted with probe stimuli. Participants were asked to choose which of two probe stimuli was expected to be presented closer to the present. Replicating prior work on JOR, we found that RT results supported a backward self-terminating search model operating on a temporally-organized representation of the past. We also showed that RT distributions are consistent with this model and that the temporally-organized representation is compressed. Critically, results for the JOI task probing expectations of the future were mirror-symmetric to results from memory, suggesting a forward self-terminating search model operating on a temporally-organized representation of the future.

animal behavior and cognition↗

bioRxiv2017

Widespread intronic polyadenylation diversifies immune cell transcriptomes

Alternative cleavage and polyadenylation (ApA) can generate mRNA isoforms with differences in 3UTR length without changing the coding region (CDR). However, ApA can also recognize intronic polyadenylation (IpA) signals to generate transcripts that lose part or all of the CDR. We analyzed 46 3-seq and RNA-seq profiles from normal human tissues, primary immune cells, and multiple myeloma (MM) samples and created an atlas of 4,927 high confidence IpA events. Up to 16% of expressed genes in immune cells generate IpA isoforms, a majority of which are differentially used during B cell development or in different cellular environments, while MM cells display a striking loss of IpA isoforms expressed in plasma cells, their cell type of origin. IpA events can lead to truncated proteins lacking C-terminal functional domains. This can mimic ectodomain shedding through loss of transmembrane domains or alter the binding specificity of proteins with DNA-binding or protein-protein interaction domains, thus contributing to diversification of the transcriptome.

genomics↗

bioRxiv2017

Recency Order Judgments In Short Term Memory: Replication And Extension Of Hacker (1980)

The classic finding from short-term relative JOR tasks is that correct response time (RT) depends on the lag to the more recent item but not to the less recent item (Hacker, 1980). For decades, researchers have argued that this finding is consistent with a self-terminating backward scanning model (Muter, 1979; Hacker, 1980; Hockley, 1984; McElree & Dosher, 1993). This finding has taken on new importance in light of recent proposal that many forms of memory depend on a compressed representation of the past (Howard, Shankar, Aue, & Criss, 2015). This paper replicates and extends the results of the classic papers. A Bayesian t-test showed substantial evidence for the null effect of lag to the less recent item on correct RT. In addition, this paper reports that correct RT is a sub-linear function of lag to the more recent probe and replicates the classic finding that error RT depends on lag to the less recent probe. These findings place new constraints on models of short-term memory scanning.

animal behavior and cognition↗

bioRxiv2017

Visual memories are stored along a compressed timeline

In continuous recognition the recency effect manifests as a decrease in accuracy and a sublinear increase in response time (RT) with the lag of a repeated stimulus. The recency effect could result from the gradual weakening of mnemonic traces. Alternatively, the recency effect could result from a search through a compressed timeline of recent experience. These two hypotheses make very different predictions about the shape of response time distributions. Using highly-memorable pictures to mitigate changes in accuracy enabled a detailed examination of the effect of recency on retrieval dynamics. The recency at which pictures were repeated ranged over two orders of magnitude across three experiments. Analysis of the RT distributions showed that the time at which memories became accessible changed with the recency of the probe, as predicted by a serial search model suggesting that visual memories can be accessed by sequentially scanning along a compressed representation of the past.

animal behavior and cognition↗