Biology subjects

Han, C.

Publications and source records attributed to Han, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

BysR, a LysR-type Pleiotropic Regulator, Controls Production of Occidiofungin by Activating the LuxR-type transcriptional regulator AmbR1 in Burkholderia sp. JP2-270

Occidiofungin is a highly effective antifungal glycopeptide produced by certain Burkholderia strains. The ocf gene cluster directing occidiofungin biosynthesis is regulated by cluster-specific regulators encoded by ambR homolog(s) within the same gene cluster, while it remains unknown to what extent occidiofungin biosynthesis is connected with the core regulation network. Here, we report that a LysR-type regulator BysR acts as a pleotropical regulator, and is essential for occidiofungin biosynthesis by directly activating ambR1 transcription in Burkholderia sp. JP2-270. Deletion of bysR and ocfE both abolished the antifungal activity in JP2-270. This defect of the bysR mutant can be recovered by constitutively expressing bysR or ambR1 but not by ambR2. The EMSA assay collectively showed that BysR regulates ambR1 through direct binding to its promoter region. Taken together, occidiofungin produced by JP2-270 is the main substance inhibiting M. oryzae, and BysR controls occidiofungin production by directly activating the expression of ambR1. Besides, transcriptomic analysis revealed altered expression of 350 genes in response to bysR deletion, and the genes engaged in flagellar assembly and bacterial chemotaxis are the most enriched pathways. Also, 400 putative loci targeted by BysR were identified by DAP-seq in JP2-270. These loci not only include genes engaged in key metabolic pathways but also genes involved in secondary metabolic pathways. Collectively, we proposes that BysR may be a novel pleiotropic regulator, and ambR1 is an important target gene of BysR, which is an intra-cluster transcriptional regulatory gene that further activates the transcription of ocf gene cluster. IMPORTANCEThis study shows that BysR, a LysR-type transcriptional regulator (LTTR) from Burkholderia sp. JP2-270, activates the expression of ambR1 gene responsible for regulating the synthesis of occidiofungin. BysR also acts as a pleiotropic regulator that controls primary and secondary metabolism, antibiotic resistance, motility, transport and other cellular processes in Burkholderia sp. JP2-270. This study provides insight into the regulatory mechanism of occidiofungin synthesis and enhances our understanding of the regulatory patterns of the LysR-type regulator.

microbiology↗

bioRxiv2022

Coordination of Pickpocket ion channel delivery and dendrite growth in Drosophila sensory neurons

Sensory neurons enable an organism to perceive external stimuli, which is essential for survival. The sensory capacity of a neuron depends on the elaboration of its dendritic arbor and the delivery of sensory ion channels to the dendritic membrane. However, it is not well understood how ion channels are trafficked to sensory dendrites and whether their delivery is coordinated with dendrite growth. We investigated the trafficking of the DEG/ENaC/ASIC ion channel Pickpocket (Ppk) in peripheral sensory neurons in fruit fly larvae. We used CRISPR-Cas9 genome engineering to tag endogenous Ppk1 and visualize it live, including monitoring Ppk1 membrane localization via a novel secreted split-GFP approach. Strikingly, Ppk1 is present throughout the membrane of actively growing dendrites, and Ppk1 density scales in proportion to the dendritic membrane, even when dynein-mediated transport to dendrites is disrupted. Our data suggest that Ppk1 is integral to the membrane of growing dendrites and implicate the recycling endosome GTPase Rab11 in the forward trafficking of Ppk1 to dendrites. Together, our results suggest that Ppk channel transport is coordinated with dendrite morphogenesis, thus ensuring proper ion channel levels and distribution in sensory dendrites. Author SummaryPeripheral sensory neurons are essential for an organism to interact with its environment. Neurons are composed of signal-receiving dendrites and a signal-sending axon. Ion channels distributed throughout sensory dendrites transduce external stimuli into chemical signals, however the mechanisms that localize ion channels to sensory dendrites are not well understood. Both the composition of ion channels in the dendrites and the structure of a sensory neurons dendritic arbor are important for how it functions to sense external stimuli. Using live imaging and genomic engineering, we have discovered that the localization of a sensory ion channel, Pickpocket, in fruit fly sensory neurons is coordinated with growth of the dendritic arbor and that Pickpocket levels scale in proportion to dendrite length, even when transport to dendrites is disrupted. We also developed a novel genetically encoded approach to visualize the membrane expression of proteins in a living organism utilizing the split-GFP system. We found that both the secretory and endosomal networks mediate the forward trafficking of Pickpocket during neuronal morphogenesis, thus coordinating membrane growth with ion channel delivery. Our findings reveal that actively growing sensory dendrites are equipped with the ion channels needed for sensing external stimuli.

neuroscience↗

bioRxiv2022

Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice.

BACKGROUNDCocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. HPTMs act combinatorically, yet few studies examine multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In the current study, we defined regulation of K4&K27 bivalency at Nr4a1 following cocaine treatment in male and female mice. The inclusion of female mice can shed light on the epidemiological relevance of sex to cocaine use disorder. METHODSMale and female mice were injected with saline or cocaine (i.p. 20mg/kg). We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). Pearsons correlation matrices quantified relationships within each brain region across treatment conditions for each sex. RESULTSWe defined K4&K27 bivalency at the Nr4a1 promoter in all three brain regions, in both sexes. In female STR, cocaine increased Nr4a1 mRNA, coupled to maintenance of Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and failed to increase Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC. CONCLUSIONThis study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice. Cocaine treatment in female mice increased Nr4a1 mRNA in STR, but there was no change in Nr4a1 H3K27me3 or K4&K27 promoter bivalency. Following cocaine treatment in male mice, Nr4a1 mRNA did not change in STR, HPC, or PFC, and Nr4a1 H3K27me3 and K4&K27 promoter bivalency increased in the STR.

neuroscience↗

bioRxiv2022

Photoperiod modulates mu-opioid receptor availability in brown adipose tissue

Photoperiod drives metabolic activity of brown adipose tissue (BAT), and affects food intake and weight gain in mammals. Sympathetic innervation in BAT controls thermogenesis and facilitates physiological adaption to seasons, but the exact mechanism remains elusive. Previous studies show that the central opioid signaling tunes BAT heating and the brain muopioid receptor (MOR) levels have seasonal patterns. It is hence intriguing to know whether the peripheral MOR signaling shows seasonal variation. Here, we examined the effect of photoperiod on BAT MOR availability using [11C]carfentanil positron emission topography (PET). Adult rats (n = 9) were repeatedly imaged under changing photoperiods which simulates the local seasons. Long photoperiod downregulated MOR availability in BAT, while MOR availability in the muscles was unaffected. We confirmed the expression of MOR in BAT and muscle using immunofluorescence imaging. We conclude that photoperiod causally affects MOR availability in BAT, and sympathetic innervation of BAT may influence thermogenesis via the peripheral MOR system. Significance of the studyPhotoperiod impacts the metabolic activity of brown adipose tissue (BAT) with the exact mechanism still unclear. The current study shows that photoperiod causally affects the mu-opioid receptor (MOR) levels in BAT, with longer photoperiod leading to lower MOR availability. This possibly indicates down-regulated innervation during bright seasons. Immunofluorescence staining data reveal expression of MOR in both brain and peripheral tissues, drawing attention to the under-investigated peripheral MOR system. Also, the study highlights the feasibility of [11C]carfentanil PET in studying the peripheral MOR signaling.

molecular biology↗

bioRxiv2022

Introducing an argonaute-facilitated PCR platform

Argonaute proteins are characterized by highly efficient guide DNA/RNA-directed binding to target nucleic acids with high fidelity. Employing this feature, we designed an argonaute-facilitated PCR platform by making use of an argonaute derived from Mesorhizobium japonicum (MejAgo) which does not carry nuclease activity and exposes the 3 end of guide DNA when binding. Each reaction cycle of the MejAgo-PCR platform consists of a denaturing step and a polymerase-mediated extension step, omitting the annealing step required by the traditional PCR. More importantly, MejAgo-PCR could significantly improve the sensitivity of PCR in template detection due to the argonaute-facilitated pairing between guide DNA/primer and template. Thus, an argonaute-facilitated PCR has the potential to be developed as an advanced PCR platform with higher sensitivity and efficiency.

biochemistry↗

bioRxiv2022

The Drosophila chemokine-like Orion bridges phosphatidylserine and Draper in phagocytosis of neurons

Phagocytic clearance of degenerating neurons is triggered by "eat-me" signals exposed on the neuronal surface. The conserved neuronal eat-me signal phosphatidylserine (PS) and the engulfment receptor Draper (Drpr) mediate phagocytosis of degenerating neurons in Drosophila. However, how PS is recognized by Drpr-expressing phagocytes in vivo remains poorly understood. Using multiple models of dendrite degeneration, we show that the Drosophila chemokine-like protein Orion can bind to PS and is responsible for detecting PS exposure on neurons; it is supplied cell-non-autonomously to coat PS-exposing dendrites and to mediate interactions between PS and Drpr, thus enabling phagocytosis. As a result, the accumulation of Orion on neurons and on phagocytes produces opposite outcomes by potentiating and suppressing phagocytosis, respectively. Moreover, the Orion dosage is a key determinant of the sensitivity of phagocytes to PS exposed on neurons. Lastly, mutagenesis analyses show that the sequence motifs shared between Orion and human immunomodulatory proteins are important for Orion function. Thus, our results uncover a missing link in PS-mediated phagocytosis in Drosophila and imply conserved mechanisms of phagocytosis of neurons. SIGNIFICANCE STATEMENTPhagocytes efficiently clear sick or damaged neuronal branches by engulfing them, while leaving healthy branches untouched. How phagocytes recognize degenerating neurites remains poorly understood. Here, we identified a key role for the secreted protein Orion in the detection and engulfment of degenerating neurites in Drosophila. Using multiple models of dendrite degeneration, we found that Orion acts as a bridging molecule between the neuronal "eat-me" signal phosphatidylserine and the engulfment receptor Draper on phagocytes, enabling phagocytosis. Our study reveals a missing link in phosphatidylserine-mediated phagocytosis in vivo, sheds light on factors determining the sensitivity of phagocytes, and implies the potential for manipulating the detection of neuronal "eat-me" signals in neurodegenerative diseases.

neuroscience↗

bioRxiv2022

A New Classification Method Based on Dynamic Ensemble Selection and its Application to Predict Variance Patterns in HIV-1 Env

Therapeutics that target the envelope glycoproteins (Envs) of human immunodeficiency virus type 1 (HIV-1) effectively reduce virus levels in patients. However, due to mutations, new Env variants are frequently generated, which may be resistant to the treatments. The appearance of such sequence variance at any Env position is seemingly random. A better understanding of the spatiotemporal patterns of variance across Env may lead to the development of new therapeutic strategies. We hypothesized that, at any time point in a patient, positions with sequence variance are clustered on the three-dimensional structure of Env. To test this hypothesis, we examined whether variance at any Env position can be predicted by the variance measured at adjacent positions. Sequences from 300 HIV-infected patients were applied to a new algorithm we developed. The k-best classifiers (KBC) method is a dynamic ensemble selection technique that identifies the best classifier(s) within the neighborhood of a new observation. It applies bootstrap resampling to generate out-of-bag samples that are used with the resampled set to evaluate each classifier. For many positions of Env, primarily in the CD4-binding site, KBC accurately predicted variance based on the variance at their adjacent positions. KBC improved performance compared to the initial learners, static ensemble, and other baseline models. KBC also outperformed other algorithms for predicting variance at multi-position footprints of therapeutics on Env. These understandings can be applied to refine models that predict future changes in HIV-1 Env. More generally, we propose KBC as a new high-performance dynamic ensemble selection technique.

bioinformatics↗

bioRxiv2022

Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages

Mutations in the spike glycoprotein of SARS-CoV-2 allow the virus to probe the sequence space in search of higher-fitness states. New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with such mutations. Interestingly, the sites of mutation in these sublineages vary between the VOCs. Whether such differences reflect the random nature of mutation appearance or distinct evolutionary spaces of spike in the VOCs is unclear. Here we show that each position of spike has a lineage-specific likelihood for mutations to appear and dominate descendent sublineages. This likelihood can be accurately estimated from the lineage-specific mutational profile of spike at a protein-wide level. The mutability environment of each position, including adjacent sites on the protein structure and neighboring sites on the network of comutability, accurately forecast changes in descendent sublineages. Mapping of imminent changes within the VOCs can contribute to the design of immunogens and therapeutics that address future forms of SARS-CoV-2.

bioinformatics↗

bioRxiv2022

A novel form of macropinocytosis mediates ultra-rapid transfer of pathological alpha- synuclein to lysosomes

The nervous system spread of alpha-synuclein fibrils is thought to cause Parkinsons disease (PD) and other synucleinopathies, yet the mechanisms underlying internalization and cellular spread are enigmatic. Here we use confocal and super-resolution microscopy, subcellular fractionation and electron microscopy (EM) of immunogold labelled alpha-synuclein preformed fibrils (PFF) to demonstrate that this fibril form of alpha-synuclein undergoes rapid internalization and is targeted directly to lysosomes in as little as 2 minutes. Uptake of PFF is disrupted by macropinocytic inhibitors and circumvents classical endosomal pathways. Immunogold-labelled PFF are seen at the highly curved inward edge of membrane ruffles, in newly formed macropinosomes, in multivesicular bodies and in lysosomes. While most fibrils remain in lysosomes, a portion is transferred to neighboring naive cells along with markers of exosomes. These data indicate that PFF use a unique internalization mechanism as a component of cell-to-cell propagation.

cell biology↗

bioRxiv2021

Single cell quantification of ribosome occupancy in early mouse development

Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key regulatory mechanism of genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high coverage measurements enabled the first analysis of allele-specific ribosome engagement in early development and led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes. Finally, by integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle stage oocytes is the predominant determinant of protein abundance in the zygote. Taken together, these findings resolve the long-standing paradox of low correlation between RNA expression and protein abundance in early embryonic development. The novel Ribo-ITP approach will enable numerous applications by providing high coverage and high resolution ribosome occupancy measurements from ultra-low input samples including single cells.

developmental biology↗

bioRxiv2021

Optogenetic operated probiotics to regulate host metabolism by mimicking enteroendocrine

The enteroendocrine system plays an important role in metabolism. The gut microbiome regulates enteroendocrine in an extensive way, arousing attention in biomedicine. However, conventional strategies of enteroendocrine regulation via gut microbiome are usually non-specific or imprecise. Here, an optogenetic operated probiotics system was developed combining synthetic biology and flexible electronics to achieve in situ controllable secretion to mimic enteroendocrine. Firstly, optogenetic engineered Lactococcus lactis (L. lactis) were administrated in the intestinal tract. A wearable optogenetic device was designed to control optical signals remotely. Then, L. lactis could secrete enteroendocrine hormone according to optical signals. As an example, optogenetic L. lactis could secrete glucagon-like peptide-1(GLP-1) under the control of the wearable optogenetic device. To improve the half-life of GLP-1 in vivo, the Fc domain from immunoglobulin was fused. Treated with this strategy, blood glucose, weight and other features were relatively well controlled in rats and mice models. Furthermore, up-conversion microcapsules were introduced to increase the excitation wavelength of the optogenetic system for better penetrability. This strategy has biomedical potential in metabolic diseases therapy by mimicking enteroendocrine.

bioengineering↗

bioRxiv2021

Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction

Natural products produced by microorganisms constitute an important source of essential pharmaceuticals, including antimicrobial and anti-tumor drugs. These bioactive molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The rapid increase of microbial genomics resources, due to the availability of high-throughput sequencing technologies, has spurred the development of computational methods for microbial genome mining for BGC discovery. Current machine learning methods, however, have limited successes in uncovering novel BGCs due to an excessive number of false positives in their predictions. To this end, we propose Deep-BGCpred, a framework that effectively addresses the aforementioned issue by improving a deep learning model termed DeepBGC. The new model embeds multi-source protein family domains and employs a stacked Bidirectional Long Short-Term Memory model to boost accuracy for BGC identifications. In particular, it integrates two customized strategies, sliding window strategy and dual-model serial screening, to improve the models performance stability and reduce the number of false positive in BGC predictions. We compare the proposed model against other well-established methods on common benchmarks and achieve new state-of-the-art results with convincing evidences. We expect that researchers working on genome mining for natural products may be greatly benefited from our newly proposed method, Deep-BGCpred.

bioinformatics↗

bioRxiv2021

Modelling novelty detection in the thalamocortical loop

In complex natural environments, sensory systems are constantly exposed to a large stream of inputs. Novel or rare stimuli, which are often associated with behaviorally important events, are typically processed differently than the steady sensory background, which has less relevance. Neural signatures of such differential processing, commonly referred to as novelty detection, have been identified on the level of EEG recordings as mismatch negativity and the level of single neurons as stimulus-specific adaptation. Here, we propose a multi-scale recurrent network with synaptic depression to explain how novelty detection can arise in the whisker-related part of the somatosensory thalamocortical loop. The architecture and dynamics of the model presume that neurons in cortical layer 6 adapt, via synaptic depression, specifically to a frequently presented stimulus, resulting in reduced population activity in the corresponding cortical column when compared with the population activity evoked by a rare stimulus. This difference in population activity is then projected from the cortex to the thalamus and amplified through the interaction between neurons of the primary and reticular nuclei of the thalamus, resulting in spindle-like, rhythmic oscillations. These differentially activated thalamic oscillations are forwarded to cortical layer 4 as a late secondary response that is specific to rare stimuli that violate a particular stimulus pattern. Model results show a strong analogy between this late single neuron activity and EEG-based mismatch negativity in terms of their common sensitivity to presentation context and timescales of response latency, as observed experimentally. Our results indicate that adaptation in L6 can establish the thalamocortical dynamics that produce signatures of SSA and MMN and suggest a mechanistic model of novelty detection that could generalize to other sensory modalities. Author summaryCortical sensory neurons have been shown to be capable of novelty detection, that is they respond more vigorously when a novel, unexpected stimulus is presented, and less so when the stimulus is part of a predictable sequence. However, the neural mechanism underlying this capability is not yet fully understood. Here, we developed a thalamocortical network model that accounts for novelty detection and reproduces physiologically observed neural response patterns in the somatosensory cortex. Specifically, our results demonstrate that the novelty signal arises from the complex recurrent interplay between thalamic neurons and cortical neurons in layers 4 and 6. This work therefore provides a concrete mechanism that can serve as a starting point for further investigating the neural circuit mechanisms underlying novelty detection.

neuroscience↗

bioRxiv2021

Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis

The chromatin state undergoes global and dynamic changes during spermatogenesis, and is critical to chromosomal synapsis, meiotic recombination, and transcriptional regulation. However, the key regulators involved and the underlying molecular mechanisms remain poorly understood. Herein we report that mouse BEND2, one of the BEN-domain-containing proteins conserved in vertebrates, was specifically expressed in spermatogenic cells within a short time-window spanning meiotic initiation, and that it plays an essential role in the progression of prophase in meiosis I. Bend2 gene knockout in male mice arrested meiosis at the transition from zygonema to pachynema, disrupted synapsis and DNA double-strand break repair, and induced non-homologous chromosomal pairing. BEND2 interacted with a number of chromatin-associated proteins--including ZMYM2, LSD1, CHD4, and ADNP-- which are components of certain transcription-repressor complexes. BEND2-binding sites were identified in diverse chromatin states and enriched in simple sequence repeats. BEND2 contributed to shutting down the mitotic gene-expression program and to the activation of meiotic and post-meiotic gene expression, and it regulated chromatin accessibility as well as the modification of H3K4me3. Therefore, our study identified BEND2 as a novel and key regulator of meiosis, gene expression, and chromatin state during mouse spermatogenesis. TeaserMeiosis is a highly complex yet poorly understood process that involves the concerted actions of an increasing number of regulators, of which the list remains incomplete. Ma et al. identified BEND2 as a novel and key regulator of meiosis and showed that it interacts with critical chromatin modulators and specific genomic elements to control the expression of mitotic and meiotic genes.

developmental biology↗

bioRxiv2021

MutS and DNA Function as a Clamp Loader for the MutL Sliding Clamp During Mismatch Repair

DNA mismatch repair (MMR) is accomplished by highly conserved MutS and MutL homologs. MutS proteins recognize mismatch nucleotides and in the presence of ATP form a stable sliding clamp on the DNA. The MutS sliding clamp then promotes the cascade assembly of a MutL sliding clamp, which ultimately coordinates downstream mismatch excision. The MutS clamp-loader mechanics are unknown. Here we have examined a conserved positively charged cleft (PCC) located on the MutL N-terminal domain (NTD) proposed to mediate stable DNA binding events in several MMR models. We show that MutL does not bind DNA in physiological ionic conditions. Instead, the MutS sliding clamps and DNA together exploit the PCC to position the MutL NTD for clamp loading. Once in a sliding clamp form, the MutL PCC aids in UvrD helicase capture but not interactions with MutH during mismatch excision. The MutS-DNA clamp-loader progressions are significantly different from the replication clamp-loaders that attach polymerase processivity factors such as {beta}-clamp and PCNA to the DNA. These studies underlining the breadth of mechanisms for stably linking crucial genome maintenance proteins to the DNA.

biophysics↗

bioRxiv2021

Coding sequence-independent homology search identifies highly divergent homopteran putative effector gene family

Homology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors. Sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall- forming aphid, Tetraneura ulmi, and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of Hormaphis cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.

evolutionary biology↗

bioRxiv2021

DNA metabarcoding Uncover the Diet of Subterranean Rodents in China

ObjectiveIn the past, the zokor, which lived in northern China, caused great harm to agriculture and forestry production due to its large and sophisticated diet. Since the rat lives underground for most of its life, researchers know little about its dietary habits. Further understanding of its diet in the field is of important meaning for developing green and sustainable control strategies for the rat. MethodsLongde County in Liupan Mountain area of Ningxia Hui Autonomous Region was selected as the interest area to capture zokor and investigate the species of habitat plants.We selected chloroplast trnL gene and eukaryotic internal transcription spacer 1 (ITS 1) primers to amplify DNA from the gastric contents of zokor,and then sequenced on Illumina Miseq PE300 platform. ResultsThe gastric contents of Eospalax smithii (n=16) and E.cansus(n=9) were analyzed by operational taxonomic units (OTU) clustering and amplicon sequence variants(ASVs).The OTU clustering method obtained 2,995 OTUs, and the ASV method obtained 4,657 ASVs. The ASV method was better than the OTU clustering method, and the ASV method was adopted in the subsequent analysis. The food list of 32 families, 80 genera and 154 species was obtained by ASV method after the error was removed. The food composition of zokor was evaluated by relative abundance(%RA) method and frequency of occurrence(%ROO) method. At the Family level, it was found that zokor mainly fed on Asteraceae, Poaceae, Rosaceae, Pinaceae, Brassicaceae, Apiaceae, etc. At the Genus level, they are mainlyEchinops, Littledalea,Artemisia,Picea, Cirsium, Elymus and so on. The diet alpha diversity of E.cansus was slightly higher than that of E.smithii (P > 0.05). The correlation coefficient between Sobs index of alpha diversity and body weight of zokor was -0.382 (P = 0.059). The diet beta diversity proved that most zokors (22/25) clustered together, with low heterogeneity. They fed positively on Calamagrostis, Cirsium, Echinops, Medicago, Sanguisorba and Taraxacum. We found that zokor mainly fed on the roots of perennial herbs(PH), which were rich in water, carbohydrate, fat and protein, which provided an important energy source for its survival. ConclusionHigh-throughput sequencing(HTS) based DNA metabarcoding technology has well revealed the diet of zokor, which are generalist.

ecology↗

bioRxiv2021

HiCImpute: A Bayesian Hierarchical Model for Identifying Structural Zeros and Enhancing Single Cell Hi-C Data.

Single cell Hi-C techniques enable one to study cell to cell variability in chromatin interactions. However, single cell Hi-C (scHi-C) data suffer severely from sparsity, that is, the existence of excess zeros due to insufficient sequencing depth. Complicate things further is the fact that not all zeros are created equal, as some are due to loci truly not interacting because of the underlying biological mechanism (structural zeros), whereas others are indeed due to insufficient sequencing depth (sampling zeros), especially for loci that interact infrequently. Differentiating between structural zeros and sampling zeros is important since correct inference would improve downstream analyses such as clustering and discovery of subtypes. Nevertheless, distinguishing between these two types of zeros has received little attention in the single cell Hi-C literature, where the issue of sparsity has been addressed mainly as a data quality improvement problem. To fill this gap, in this paper, we propose HiCImpute, a Bayesian hierarchy model that goes beyond data quality improvement by also identifying observed zeros that are in fact structural zeros. HiCImpute takes spatial dependencies of scHi-C 2D data structure into account while also borrowing information from similar single cells and bulk data, when such are available. Through an extensive set of analyses of synthetic and real data, we demonstrate the ability of HiCImpute for identifying structural zeros with high sensitivity, and for accurate imputation of dropout values in sampling zeros. Downstream analyses using data improved from HiCImpute yielded much more accurate clustering of cell types compared to using observed data or data improved by several comparison methods. Most significantly, HiCImpute-improved data has led to the identification of subtypes within each of the excitatory neuronal cells of L4 and L5 in the prefrontal cortex.

genetics↗