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Biology subjects

Mukherjee, I.

Publications and source records attributed to Mukherjee, I..

15 recordsLinked to original sources

Energetics and behavior during predation in wild, schooling white mullet (Mugil curema)

Although predation is a major driver of group living across taxa and the antipredator benefits of grouping are well established, the energetic costs experienced by groups under predation remain largely unexplored. In the current study, we use wild, white mullet (Mugil curema, Valenciennes 1836), to provide the first real-time quantification of the energetic cost of escape in schooling fish using intermittent, closed-loop respirometry. We found that small groups exposed to predators showed a 53.8% increase in their organismal metabolic rate (MO2) as compared to groups without predator exposure. When we evaluated antipredator behaviors such as escape response, group cohesion, and displacement of the group centroid, we found a positive correlation to energetic costs. We then investigated whether escape responses are socially modulated by comparing the energetic costs of escape across solitary individuals, solitary individuals with visual access to a group, and groups. We found that escape frequency and energetic costs to predation were comparable across social contexts, indicating that escape may be an intrinsic survival response independent of cues from group members. Furthermore, we found that fish exposed to predators showed markedly reduced feeding, suggesting that predation constrains energy acquisition in addition to imposing direct energetic costs. Our results provide the first direct quantification of the energetic costs of escape in a schooling fish, offering new insights into the physiological trade-offs underlying collective antipredator defenses.

animal behavior and cognition↗

High-temporal resolution of microbial food web dynamics and structure during phytoplankton blooms in the Baltic Sea

Heterotrophic nanoflagellates (HNF) are a key component of the microbial food webs, playing an essential role in nutrient recycling and energy transfer in aquatic ecosystems. They have been typically considered to be bacterivores, but they can be also omnivorous (feeding on prokaryotes and other eukaryotes) and predatory grazers (feeding on other eukaryotes). Here, we combine CARD-FISH with both short and long-amplicon sequencing to resolve dynamics of key HNF groups during two high-frequency sampling campaigns in spring (March-May) and autumn (September-November) phytoplankton blooms in the coastal waters of the Baltic Sea. This approach allowed us to resolve the microbial food web dynamics within HNF communities at the phylotype level at time scales relevant to HNF duplication times. Omnivorous katablepharids and predatory MAST-2 dominated the HNF community, especially in spring. Bacterivorous groups (e.g., MAST-1, CRY1) were less abundant. Long-read sequencing revealed distinct seasonal shifts in dominant phylotypes, with Katablepharis sp. and MAST-2D peaking in spring, while other lineages became more prominent in summer and autumn. The high abundance of omnivorous HNF, compared to bacterivores, highlights their key role both as grazers of bacteria and flagellates and as a food source for predatory and omnivorous ciliates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/676335v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@c4ec55org.highwire.dtl.DTLVardef@77fd5dorg.highwire.dtl.DTLVardef@19b237borg.highwire.dtl.DTLVardef@368f39_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

Season-specific responses of freshwater ciliate communities to top-down and bottom-up experimental manipulations

In aquatic microbial food webs, ciliates represent an important trophic link in the energy transfer from prokaryotes, algae, and heterotrophic nanoflagellates (HNF) to higher trophic levels. However, the trophic role of abundant small ciliates (< 20 {micro}m) is not clearly understood. To unveil their trophic linkages, we conducted two experiments manipulating both top-down and bottom-up controlling factors, thus modulating the trophic cascading and bacterial prey availability for protists during contrasting spring and summer seasons with samples collected from a freshwater meso-eutrophic reservoir. Water samples were size fractionated, to modify food web complexity, i.e. 10-{micro}m, 20-{micro}m and unfiltered control and amended with bacterial prey additions. The samples were analyzed by morphological and sequencing techniques. The bacterial amendments triggered strong ciliate growth following the peaks of HNF in the 10-{micro}m and 20-{micro}m treatments, reflecting a trophic cascading from HNF to raptorial prostome ciliates (Balanion planctonicum and Urotricha spp.) in spring. In summer, HNF and ciliates peaked simultaneously, suggesting the important trophic cascade from bacteria to bacterivorous scuticociliates (Cyclidium glaucoma and Cinetochilum margaritaceum) and HNF. In spring, unfiltered treatments showed stronger ciliate top-down control by zooplankton than in summer. The sequence analysis revealed season-specific manipulation-induced shifts in ciliate communities and their large cryptic diversity. However, morphological and molecular analyses also revealed considerable discrepancies in the abundance of major ciliate taxa. The ciliate communities responded to our experimental manipulations in season-specific fashion, thereby highlighting the different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. IMPORTANCECiliates are an important trophic link in aquatic microbial food webs. In this study, we used the food web manipulation techniques to reveal their complex trophic interactions during seasonally different plankton scenarios occurring in spring and summer. Manipulating top-down controlling factors (grazing pressure of micro- and metazooplankton grazers) and bottom-up factors (an availability of bacterial prey) shaped distinctly the complexity and dynamics of natural plankton communities and thus yielded significant changes in ciliate community dynamics. The experimentally simplified plankton and ciliate communities responded to our manipulations in season-specific fashions, reflected in different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. This study also demonstrates that the combination of morphological and molecular analyses is essential for providing robust and ecologically meaningful results due to the reliability in quantifying the major ciliate taxa and their trophic role.

ecology↗

Localization and function of key axonemal microtubule inner proteins and dynein docking complex members reveal extensive diversity among vertebrate motile cilia

Vertebrate motile cilia are broadly classified as (9+2) or (9+0), based on the presence or absence of the central pair apparatus, respectively. Cryogenic electron microscopy (cryo-EM) analyses of (9+2) cilia have uncovered an elaborate axonemal protein composition; whether these features are relevant to (9+0) cilia remain unclear. We previously demonstrated that Cfap53, a key microtubule inner protein (MIP) as well as centriolar-satellites component, is essential for motility of (9+0), but not (9+2) cilia. Here, we show that in (9+2) cilia, Cfap53 functions redundantly with a paralogous MIP, Mns1. Mns1 localizes to ciliary axonemes, and combined loss of both proteins in zebrafish and mice, caused severe loss of outer dynein arms (ODAs) of (9+2) cilia, significantly affecting their motility. Moreover, using immunoprecipitation, we demonstrate that while Mns1 can self-associate and interact with Cfap53, Cfap53 is unable to self-associate. Finally, we show that multiple additional dynein interacting proteins, such as the ODA docking complex (ODA-DC) members, show strikingly distinct localization patterns between various motile cilia-types. Our findings clarify how paralogous MIPs, Cfap53 and Mns1, function in regulating motility of (9+2) versus (9+0) cilia, and establish that localization pattern of other key motility proteins also differ between these cilia-types, further emphasizing extensive structural variations among these organelles.

developmental biology↗

Depth-dependent dynamics of protist communities as an integral part of spring succession in a freshwater reservoir

BackgroundProtists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of [R]imov reservoir, Czech Republic. Over a two-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. ResultsFollowing the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transition from a homogeneous community to distinct strata-specific communities. Epilimnion exhibited the prevalence of auto-, mixotrophic protists dominated by cryptophytes and associated with spring algal bloom-specialized bacteria. In contrast, meta- and hypolimnion showcased the development of protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans and excavate protists co-occurring with bacteria associated with lake snow. ConclusionsOur high-resolution sampling matching the typical dividing time of microbes along with the combined microscopic and molecular approach and inclusion of all the components of microbial food web allowed us to follow depth-specific populations successions and interactions in a deep lentic ecosystem.

ecology↗

Hiding in the bush, in fear of a predator! Vegetation and predators influence shoaling among wild zebrafish

Social responses of aquatic group-living organisms are critically dependent on predation risk and vegetation cover in their habitat. To gain insight into how these factors shape their immediate responses, we exposed wild zebrafish shoals to either vegetation, predator cues or both these factors simultaneously. Control treatments were not exposed to the above factors. By analyzing 60 unique shoals across 270 experimental trials, we found that while shoals formed significantly larger subgroups and were significantly more polarized in the presence of predator cues, both these properties decreased when shoals experienced predator cues in presence of vegetation. Furthermore, foraging was significantly lower when predator cues and/or vegetation were present. Tracking of all individuals in treatments devoid of vegetation revealed that: (i) compared to control treatments, individuals within shoals receiving predator cues had a significantly higher probability to continue being in a group and (ii) individuals occupying the front positions deviated lesser from their median position within a shoal as compared to other individuals. Anti-predator responses and foraging are critical for survival and therefore, this study provides important insights into shoal dynamics in changing environments.

animal behavior and cognition↗

Rickettsiales' deep evolutionary history sheds light on the emergence of intracellular lifestyles

Ancient bacteria largely lived and flourished as free-living cells till the rise of eukaryotes triggered their adaptation to a new habitat: the intracellular milieu. Rickettsiales bacteria are the most prevalent intracellular microorganisms discovered and the culprits behind some of mankinds worst pestilential diseases. Here, we show that intracellularity is not a defining feature of the group and describe the eco-evolutionary processes that transformed harmless free-living bacteria into obligate intracellular symbionts and parasites. We found that the evolution of free-living lineages towards enhanced cross-feeding interactions with microbial eukaryotes trapped them in a nutritional bind to their trophic partners. We discovered that the oldest Rickettsiales lineages are the closest relatives to modern eukaryotes and are enriched in proteins predicted to have been present in the mitochondrial ancestor. This study not only opens avenues for the detection and surveillance of emerging diseases but also expands our understanding of the origins of complex life. One-Sentence SummaryCross-feeding interactions shaped Rickettsiales genomic architectures along the parasite/free-living spectrum

microbiology↗

Use of multimodal sensory cues in predator avoidance by wild-caught zebrafish shoals

Shoaling in fishes is regulated by factors like predation, vegetation cover, water flow and food availability. Shoals detect and respond to changes in these ecological factors using a multimodal sensory system. Here, we examine the immediate response of wild-caught zebrafish (Danio rerio) shoals to cues from its natural predator, the snakehead (Channa sp.). Zebrafish shoals were recorded upon exposure to (1) olfactory predator cues, (2) visual predator cues, (3) both cues together, and (4) no cue. We tracked individuals and analysed shoal responses across these treatments. We found that compared to control treatments, shoals receiving either visual or olfactory cues had significantly greater: (i) cohesion, (ii) polarization and (iii) velocity. Interestingly, when the shoals received both cues simultaneously, the cohesion, polarization and velocity decreased and a significantly greater number of individual freezing events occurred. Therefore, zebrafish relied on both visual and olfactory cues to escape predation. However, when shoals were presented with both cues together, while freezing frequency increased, other responses were comparable to control treatments where no predator cue was provided. While this study indicates that multimodal cues elicit a different anti-predator response than the cues singly, more experiments are required to identify the underlying cause of this behaviour.

animal behavior and cognition↗

What drives mixed-species shoaling among wild zebrafish? Role of predators, food access, abundance of conspecifics, and kin familiarity

Mixed-species groups commonly occur across a wide range of faunal communities and are known to provide several benefits to members. While zebrafish have often been observed to form mixed-species shoals with coexisting species, the factors determining their occurrence is not yet understood. Using laboratory-based experiments, we decipher the main ecological drivers of mixed-species shoaling in these tropical fish communities. Shoals comprising zebrafish (Danio rerio), flying barbs (Esomus danricus) and whitespots (Aplocheilus panchax) were collected from a stagnant canal at Haringhata (West Bengal, India). Experiments to assess foraging efficiency were conducted where single or mixed-species shoals (comprising 5 individuals) were given low or high amounts of food. Shoal choice experiments were also conducted to assess the preferences of test subjects (zebrafish individuals) for forming associations based on shoal composition and familiarity. Results from experiments on feeding efficiency revealed that foraging time varied substantially among the shoal types (i.e., single or mixed-species), and was dependent on the quantity of food available, but not linked to the body size of species composing the shoal. The choice experiments to examine preference for associations revealed that under predator risk, zebrafish associate more with mixed shoals, and showed comparable associations to shoals differing in the abundance of conspecifics. Furthermore, we found that zebrafish preferred to associate with familiar conspecific over unfamiliar mixed and unfamiliar conspecific shoals. Therefore, equitable food consumption in mixed shoals, greater association to mixed shoals in presence of predator and familiarity were found to be important drivers for choosing mixed-species shoaling by zebrafish.

animal behavior and cognition↗

Target-Dependent Coordinated Biogenesis Ensure Cascaded Expression of miRNAs in Activated Macrophage

MicroRNAs (miRNAs) repress protein expression by binding to the 3 UTR of the target mRNAs. By exploring the effect of target mRNA on biogenesis of cognate miRNAs, we have noted miRNA with higher number of binding sites (primary miRNA) coordinates the biogenesis and activity of another miRNA (secondary miRNA) having binding sites on the 3 UTR of a common target mRNA. From the quantitative data obtained from macrophage cells, we detected miR-146a-5p as a "primary" miRNA that coordinates biogenesis of "secondary" miR-125b, miR-21 or miR-142-3p to target new sets of mRNAs to balance the immune response in activated macrophage cells. Interestingly, target dependent coordinated biogenesis of miRNAs, happening on the rough endoplasmic reticulum attached membrane, ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs where a cascaded effect of primary miRNA on its secondary targets has been detected. Extensive computational analysis for the presence of coordinated biogenesis pairs of miRNAs in mammalian cells has also allowed us to construct a coordinate biogenesis repository to determine context specific coordinated biogenesis relationships exists for specific pairs of miRNAs in mammalian cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/448041v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@318871org.highwire.dtl.DTLVardef@1f4d3a3org.highwire.dtl.DTLVardef@72adceorg.highwire.dtl.DTLVardef@f0d79e_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LImiRNA with higher number of binding sites (primary miRNA) can coordinates the biogenesis and activity of another miRNA (secondary miRNA) C_LIO_LITarget dependent coordinated biogenesis of miRNAs ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs on rER attached polysomes C_LIO_LImiR-146a-5p acts as a "primary" miRNA to coordinate biogenesis of "secondary" miR-125b, miR-21 or miR-142-3p in activated macrophage cells C_LIO_LICoordinate biogenesis balance the immune response in activated macrophage cells by ensuring propagation of primary miRNAs effect to diverse target mRNAs through secondary miRNAs. C_LI

molecular biology↗

Rheb-mTOR Activation Rescues Amyloid Beta-Induced Cognitive Impairment and Memory Function by Restoring miR-146 Activity in Glial Cells

Deposition of amyloid beta plaques in adult rat or human brain is associated with increased production of proinflammatory cytokines by associated glial cells that are responsible for degeneration of the diseased tissue. The expression of these cytokines is usually under check and is controlled at post-transcriptional level via several microRNAs. Computational analysis of gene expression profiles of cortical regions of Alzheimers disease patients brain suggests ineffective target cytokine mRNA suppression by existing microRNPs in diseased brain. Exploring the mechanism of amyloid beta induced cytokine expression, we have identified how the inactivation of the repressive miR-146 microRNPs causes increased production of cytokines in amyloid beta exposed glial cells. In exploration of the cause of miRNP inactivation, we have noted amyloid beta oligomer induced sequestration of mTORC1 complex to early endosomes that results in decreased Ago2 phosphorylation, limited Ago2-miRNA uncoupling and retarded Ago2-cytokine mRNA interaction in rat astrocyte cells. Interestingly, constitutive activation of mTORC1 by Rheb activator restricts proinflammatory cytokine production by reactivating miR-146 microRNPs in amyloid beta exposed glial cells to rescue the disease phenotype in the in vivo rat model of Alzheimers disease.

neuroscience↗

Co-evolutionary Landscape at the Interface and Non-Interface Regions of Protein-Protein Interaction Complexes

Proteins involved in interactions throughout the course of evolution tend to co-evolve and compensatory or coordinated changes may occur in interacting proteins to maintain or refine interactions between them. However, certain residue pair alterations may prove to be detrimental for functional interactions. Hence, determining co-evolutionary pairings that could be structurally or functionally relevant for maintaining the conservation of an inter-protein interaction is important. Inter-protein co-evolution analysis in a number of complexes with the help of multiple existing methodologies suggested that co-evolutionary pairings can occur in spatially proximal as well as distant regions of inter-protein interaction complexes. Subsequently, the Co-Var (Correlated Variation) method based on mutual information and Bhattacharyya coefficient was developed, validated and found to perform relatively better than CAPS and EV-complex. Interestingly, while applying the Co-Var measure on a set of protein-protein interaction complexes, co-evolutionary pairings were obtained in spatially proximal and distant regions in inter-protein complexes. Our approach involves determining high degree co-evolutionary pairings which include multiple co-evolutionary connections between particular co-evolved residue positions in one protein and particular residue positions in the binding partner. Detailed analyses of high degree co-evolutionary pairings in protein-protein complexes involved in inter-cellular communication during cancer metastasis were performed. These analyses suggested that most of the residue positions involved in such co-evolutionary pairings mainly occurred within functional domains of constituent proteins and substitution mutations were also common among these co-evolved positions. The physiological relevance of these predictions suggests that Co-Var can predict residues that could be crucial for preserving functional protein-protein interactions. Finally, Co-Var web server that implements this methodology was developed. This web server available at http://www.hpppi.iicb.res.in/ishi/covar/index.html identifies co-evolutionary pairings in intra-protein and inter-protein complexes.

bioinformatics↗

Lipid Droplets Promote Phase Separation of Ago2 to Accelerate Dicer1 Loss and Decelerate miRNA Activity in Lipid Exposed Hepatic Cells

miR-122 is a liver specific miRNA that plays an important role in controlling metabolic homeostasis in mammalian liver cells. Interestingly, miR-122 on exposure to lipotoxic stress is reduced in liver cells. To fight stress, miRNA processor Dicer1 is depleted to cause reduced miR-122 production and the lowering of miRNA level ensures a better stress response in hepatocytes under lipotoxic stress. Interestingly, lipid droplets, formed in the liver cells on exposure to high fat, ensure cytoplasmic phase separation of Ago2 and prevent interaction of Ago2 with Dicer1. Lipid droplets bind miRNA and enhance miRNA-Ago2 uncoupling and Ago2 phase separation. Loss of interaction between Ago2 and Dicer1 eventually facilitates export and lowering of cellular Dicer1, a process also dependent on the endosomal maturation controller protein Alix, thereby ceasing pre-miRNA processing by Dicer1 in lipid exposed cells. Depletion of lipid droplets by downregulation of Perilipins with siRNAs resulted in a rescue of cellular Dicer1 level and Ago2-Dicer1 interaction. This is a novel mechanism that liver cells adopt to restrict cellular miRNA levels under stress condition. Thus, lipid droplets prevent cell death upon exposure to high fat by reducing intra and extracellular pool of miR-122 in hepatic tissue.

cell biology↗

Genotypic and antigenic study of SARS-CoV-2 from an Indian isolate.

Coronaviruses (CoVs) are one of the largest groups of positive-sense RNA virus families within the Nidovirales order, which are further classified into four genera: alpha, beta, gamma, and delta. Coronaviruses have an extensive range of natural hosts and are known to be responsible for a broad spectrum of diseases in multiple species. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) that has unleashed a global threat to public health and the economy. Coronaviruses are extensively present in birds and mammals, with horseshoe bats (Rhinolophus affinis), being the reservoir for the ongoing SARS-CoV-2 that seems to have resulted from a zoonotic spillover to the human host, causing respiratory infections, lung injury and Acute Respiratory Distress Syndrome(ARDS). About six coronavirus serotypes are linked with the disease in humans, namely HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, SARS-CoV-2, and MERS-CoV. SARS-CoV-2 is the seventh CoV to infect humans. We analyzed the genome sequence of CoV-2 from isolates derived from China as well from India and encountered minute variations in their sequence. A cladogram analysis revealed the predominant strain circulating in India belongs to the A2a clad. We took one such strain (MT012098) and performed a rigorous in-silico genotypic and antigenic analysis to identify its relatedness to other strains. Further, we also performed a detailed prediction for B and T cell epitopes using BepiPred 2.0 server and NetCTL 1.2 server (DTU Bioinformatics), respectively. We hope this information may assist in an effective vaccine designing program against SARS-CoV-2.

biochemistry↗

A freshwater radiation of diplonemids

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and CARD-FISH. We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to marine isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single cell genomes of marine diplonemids shows they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.

microbiology↗