Biology subjects

Kaufman, M.

Publications and source records attributed to Kaufman, M..

11 recordsLinked to original sources

bioRxiv2025

Sea-ice microbial community succession and the potential role of parasitoids in the maintenance of diversity

Sea ice is a crucial, yet declining, habitat in high latitude ecosystems. Here we present a high-temporal resolution amplicon sequence data set collected during the spring ice-algal bloom near Utqia[g]vik, Alaska in 2021 to study sea-ice microbial dynamics. The ice-algal bloom peaked on May 8th, reaching 46.6 mg chlorophyll a m-2, and thereafter became limited by nitrate availability. A massive bloom of the oil-degrading bacterium, Oleispira (>80% relative abundance), coincided with the algal bloom raising questions about hydrocarbon exposure. The sea-ice algal bloom was dominated by diatoms, particularly Nitzschia spp., and transitioned into a flagellate dominated post-bloom community which aligned with melt-associated changes to the physicochemical environment. We explored the relationship between putative parasitoids, Chytridiomycetes, Thecofilosea (Cercozoa), Oomycetes, Syndiniales (Dinoflagellata), and Labyrinthulomycetes (Bigyra), and potential microalgal hosts. Chytrids peaked periodically suggesting synchronized infections and Cryothecomonas (Thecofilosea) was observed parasitizing Nitzschia spp. for the first time in Arctic sea ice. Co-occurrence analysis suggested that diatoms, especially Nitzschia, were the primary hosts of Pacific-Arctic parasitoids, and that top-down parasitoid control may dramatically alter community composition over short timescales, such as days. These results provide important insights into the drivers of spring bloom timing and maintenance of microalgal diversity in sea ice.

microbiology↗

bioRxiv2025

Mouse sensorimotor cortex reflects complex kinematic details during reaching and grasping

Coordinated forelimb actions, such as reaching and grasping, rely on motor commands that span a spectrum from abstract target specification to detailed instantaneous muscle control. The sensorimotor cortex is central to controlling these complex movements, yet how the detailed command signals are distributed across its numerous subregions remains unclear. In particular, in mice it is unknown if the primary motor (M1) and somatosensory (S1) cortices represent low-level joint angle details in addition to high-level signals like movement direction. Here, we combine high quality markerless tracking and two-photon imaging during a reach-to-grasp task to quantify movement-related activity in the mouse forelimb M1 (M1-fl) and forelimb S1 (S1-fl). Linear decoding models reveal a strong representation of proximal and distal joint angles in both areas, and both areas support joint angle decoding with comparable fidelity. Despite shared low-level encoding, the time course of high-level target-specific information varied across areas. M1-fl exhibited early onset and sustained encoding of target-specific signals while S1-fl was more transiently modulated around lift onset. These results reveal both shared and unique contributions of M1-fl and S1-fl to reaching and grasping, implicating a more distributed cortical circuit for mouse forelimb control than has been previously considered.

neuroscience↗

bioRxiv2024

Sediment-associated processes drive spatial variation in ecosystem respiration in the Yakima River basin

Hyporheic zones (HZ) can contribute substantially to total stream ecosystem respiration (ERtot). HZ-focused process-based models may, therefore, effectively predict ERtot across sites, yet this remains untested under variable environmental conditions. Here we evaluate whether spatial variation in HZ respiration predicted via a process-based model explains spatial variation in field-estimates of ERtot across 33 sites in the Yakima River basin in Washington State, USA. We found that HZ respiration predictions did not explain spatial variation in field estimates of ERtot. To investigate further, we partitioned ERtot contributions into water column respiration (ERwc) and sediment-associated respiration (ERsed). ERsed contributed >50% of ERtot at 88% of sites, though relative contributions varied substantially. Despite this dominance, modeled HZ respiration explained neither spatial variation in ERtot nor in ERsed, suggesting that the HZ model alone does not capture the drivers of sediment-associated respiration across these sites. Instead, ERsed spatial variation was primarily explained by gross primary production, stream slope, velocity, and total dissolved nitrogen rather than median grain size, a primary control of HZ respiration predicted by the process-based model. Consistent with recent studies, our results indicate that improving basin-scale ERtot predictions requires integrating hydrologic and biogeochemical processes across hyporheic, benthic, and water column zones.

ecology↗

bioRxiv2024

Oxytocin signaling regulates maternally-directed behavior during early life

Oxytocin is essential in shaping social behavior across the lifespan. While the role of oxytocin signaling in parental care has been widely investigated, little is known about its function in social behavior during early life. This is partly due to the lack of precise technologies for studying the developing brain. Here, we studied the role of oxytocin in pup social behavior under acute separation from and reunion with the mother. We show that the activity of oxytocin neurons was increased by acute maternal separation and returned to baseline after reunion. Behaviorally, maternally-separated pups emitted more ultrasonic vocalizations upon reunion, which were further modulated by nipple attachment behavior. These effects were attenuated by blocking the oxytocin receptor during maternal separation. To investigate the role of oxytocin neurons with higher precision, we established a method for transcranial optogenetic silencing of neuronal activity in untethered and freely behaving pups. Using this approach, we found that silencing of oxytocin neurons during maternal separation disrupted vocal behavior during separation and reunion in a sex-specific manner. Our findings reveal an important role of oxytocin in context-dependent vocal communication in pups, offering new insights into the mechanisms of social behavior during early life.

neuroscience↗

bioRxiv2023

Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments

We present a system for carrying out small batch reactor microbial metabolism experiments on water and sediment samples for environmental questions. In general, it provides several advantages that can help researchers achieve impactful experiments at relatively low costs and high data quality. In particular, it allows for multiple reactors to be operated and their oxygen concentrations to be measured simultaneously, providing high throughput and high time-resolution data, which can be advantageous. Most existing literature on similar small batch-reactor metabolic studies is limited to either only a few samples, or only a few time points per sample, which can restrict the ability for researchers to learn from their experiments. The oxygen sensing system is based very directly on the work of Larsen, et al. [2011], and similar oxygen sensing technology is widely used in the literature. As such we do not delve deeply into the specifics of the fluorescent dye sensing mechanism. Instead, we focus on practical considerations. We describe the construction and operation of the calibration and experimental systems, and answer many of the questions likely to come up when other researchers choose to build and operate a similar system themselves (questions we ourselves had when we first built the system). In this way, we hope to provide an approachable and easy to use research article that can help other researchers construct and operate a similar system that can be tailored to ask their own research questions, with a minimum of confusion and missteps along the way.

biochemistry↗

bioRxiv2022

An ecological investigation of the capacity to follow simultaneous speech and preferential detection of ones' own name

Many situations require focusing attention on one speaker, while monitoring the environment for potentially important information. Some have proposed that dividing attention among two speakers involves behavioral tradeoffs, due to limited cognitive resources. However the severity of these tradeoffs, particularly under ecologically-valid circumstances, is not well understood. We investigated the capacity to process simultaneous speech using a dual-task paradigm simulating task demands and stimuli encountered in real-life. Participants listened to conversational narratives (Narrative Stream) and monitored a stream of announcements (Barista Stream), to detect when their order was called. We measured participants performance, neural activity and skin conductance as they engaged in this dual-task. Participants achieved extremely high dual-task accuracy, with no apparent behavioral tradeoffs. Moreover, robust neural and physiological responses were observed for target-stimuli in the Barista Stream, alongside significant neural speech-tracking of the Narrative Stream. These results suggest that humans have substantial capacity to process simultaneous speech and do not suffer from insufficient processing resources, at least for this highly ecological task-combination and level of perceptual load. Results also confirmed the ecological validity of the advantage for detecting ones own name at the behavioral, neural and physiological level, highlighting the contribution of personal relevance when processing simultaneous speech.

neuroscience↗

bioRxiv2022

Capacity and tradeoffs in neural encoding of concurrent speech during Selective and Distributed Attention

Speech comprehension is severely compromised when several people talk at once, due to limited perceptual and cognitive resources. Under some circumstances listeners can employ top-down attention to prioritize the processing of task-relevant speech. However, whether the system can effectively represent more than one speech input remains highly debated. Here we studied how task-relevance affects the neural representation of concurrent speakers under two extreme conditions: when only one speaker was task-relevant (Selective Attention), vs. when two speakers were equally relevant (Distributed Attention). Neural activity was measured using magnetoencephalography (MEG) and we analysed the speech-tracking responses to both speakers. Crucially, we explored different hypotheses as to how the brain may have represented the two speech streams, without making a-priori assumptions regarding participants internal allocation of attention. Results indicate that neural tracking of concurrent speech did not fully mirror their instructed task-relevance. When Distributed Attention was required, we observed a tradeoff between the two speakers despite their equal task-relevance, akin to the top-down modulation observed during Selective Attention. This points to the systems inherent limitation to fully process two speech streams, and highlights the complex nature of attention, particularly for continuous speech.

neuroscience↗

bioRxiv2021

Hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) expression and signaling promotes the maintenance of an immunoinhibitory retinal environment

BackgroundExcessive oxidative stress and related chronic, sub-clinical inflammation is linked causally to the development and progression of degenerative diseases of the retina including diabetic retinopathy, age-related macular degeneration and glaucoma, leading causes of blindness worldwide. The above responses may be related directly to dysregulated retinal immunity and are potentiated by the combined actions of native retinal cells (e.g., retinal pigment epithelial (RPE) and microglial cells) and immune cells infiltrating from the periphery. Maintaining tight regulation of these cells such that effective control of pathogens is accomplished yet uncontrolled inflammation and consequent tissue damage is prevented is extremely important. However, the molecular mechanisms that control this delicate balance are poorly understood. We hypothesize that the hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) may play an important role. HCAR2/GPR109A has been shown to regulate immune cell responses that potentiate anti-inflammatory signaling upon its activation in various tissues as evidenced principally by suppressed pro-inflammatory cytokine secretion in various experimental model systems. We have demonstrated HCAR2/GPR109A expression in RPE, microglia and endothelial cells and, our in vitro studies support that the receptor elicits anti-inflammatory signaling in these cell types. However, the functional relevance of HCAR2/GPR109A expression and its activation in the retina of the living animal has not been demonstrated definitively. This is the purpose of the present study. MethodsRetinal function was evaluated temporally in wildtype (Hcar2/Gpr109a +/+, WT) and knockout (Hcar2/Gpr109 -/-, KO) mice via electroretinography (ERG). Fundoscopic imaging, spectral domain-optical coherence tomography (OCT), fluorescein angiography and post-mortem histological analyses were additionally performed to evaluate retinal health. Gene microarray, RT-qPCR studies, ingenuity analyses and proteome pathway mapping were performed to evaluate potential key differences in the molecular signatures of WT and KO mouse retinas. Leukostasis and flow cytometric assays were performed to demonstrate the in vivo impact of HCAR2/GPR109A expression and its therapeutic activation on pro-inflammatory immune cell trafficking in retina. ResultsLongitudinal studies revealed progressive anomalies in retinal morphology and function in HCAR2/GPR109A knockout mice that impacted the entire retina. Gene expression and protein interactome analyses revealed differences in gene and protein expression consistent with the increased immune reactivity and infiltration of bone-marrow derived immune cells detected in KO mouse retinas. Studies conducted in an acute model of retinal (endotoxin-induced) inflammation revealed that targeting the receptor via intraperitoneal administration of agonist, beta-hydroxybutyrate, limits immune cell activation, infiltration and related inflammation in WT retinas. ConclusionsThe present studies demonstrate a central role for HCAR2/GPR109A in regulating the complex interplay between resident retinal cells and peripheral immune cells and, the potential therapeutic utility that targeting the receptor holds with respect to preventing and treating inflammatory retinal diseases. HighlightsOxidative stress and inflammation are major causative factors in degenerative retinal diseases stemming from numerous causes (e.g., aging, diabetes, sickle cell). Thus, identifying new targets and developing strategies to counter these factors to prevent and treat retinal degeneration is important. The present in vivo study demonstrates convincingly the principal role of the hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) as a major regulator of retinal immune responses under normal conditions and therefore, as a target with extremely high potential for therapeutic modulation of these responses in retinal disease.

biochemistry↗

bioRxiv2018

Dynamics of social representation in the mouse prefrontal cortex

The prefrontal cortex (PFC) plays an important role in regulating social functions in mammals, and impairments in this region have been linked with social dysfunction in psychiatric disorders. Yet little is known of how the PFC encodes social information and of how social representations may be altered in such disorders. Here, we show that neurons in the medial PFC (mPFC) of freely behaving mice preferentially respond to socially-relevant sensory cues. Population activity patterns in the mPFC differed considerably between social and nonsocial stimuli and underwent experience-dependent refinement. In Cntnap2 knockout mice, a genetic model of autism, both the categorization of sensory stimuli and the refinement of social representations were impaired. Noise levels in spontaneous population activity were higher in Cntnap2 mice, and correlated strongly with the degree to which social representations were disrupted. Our findings elucidate the encoding of social sensory cues in the mPFC, and provide an important link between altered prefrontal dynamics and autism-associated social dysfunction.

neuroscience↗

bioRxiv2017

Accurate estimation of neural population dynamics without spike sorting

A central goal of systems neuroscience is to relate an organisms neural activity to behavior. Neural population analysis often begins by reducing the dimensionality of the data to focus on the patterns most relevant to a given task. A major practical hurdle to data analysis is spike sorting, and this problem is growing rapidly as the number of neurons measured increases. Here, we investigate whether spike sorting is necessary to estimate neural dynamics. The theory of random projections suggests that we can accurately estimate the geometry of low-dimensional manifolds from a small number of linear projections of the data. We re-analyzed data from three previous studies and found that neural dynamics and scientific conclusions are quite similar using multi-unit threshold crossings in place of sorted neurons. This finding unlocks existing data for new analyses and informs the design and use of new electrode arrays for laboratory and clinical use.

neuroscience↗

bioRxiv2017

OnACID: Online Analysis of Calcium Imaging Data in Real Time

Optical imaging methods using calcium indicators are critical for monitoring the activity of large neuronal populations in vivo. Imaging experiments typically generate a large amount of data that needs to be processed to extract the activity of the imaged neuronal sources. While deriving such processing algorithms is an active area of research, most existing methods require the processing of large amounts of data at a time, rendering them vulnerable to the volume of the recorded data, and preventing realtime experimental interrogation. Here we introduce OnACID, an Online framework for the Analysis of streaming Calcium Imaging Data, including i) motion artifact correction, ii) neuronal source extraction, and iii) activity denoising and deconvolution. Our approach combines and extends previous work on online dictionary learning and calcium imaging data analysis, to deliver an automated pipeline that can discover and track the activity of hundreds of cells in real time, thereby enabling new types of closed-loop experiments. We apply our algorithm on two large scale experimental datasets, benchmark its performance on manually annotated data, and show that it outperforms a popular offline approach.

neuroscience↗