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Community detection in dynamic networks is of great importance in social network analysis. For instance, online social networks such as Facebook, WhatsApp and LinkedIn are rapidly evolving with time. However, the majority of previous research have focused on community detection in static networks. It is computationally expensive to repeatedly use a static algorithm on snapshots of dynamic networks. In this paper, we propose a community detection algorithm namely, Tie Strength based Incremental Community detection (TSInc), aiming to find communities and track the dynamic events in each snapshot. TSInc determines communities using tie strength based information cascades. Following the initial snapshot, we construct a new subgraph based on the dynamic events in the subsequent snapshots and quickly assign communities. These communities in combination with the unchanged communities are merged to obtain the inherent community structure. These procedure is repeated for the remaining snapshots as well. Experimental results on several real-world dynamic networks and state-of-the-art approaches shows that TSInc algorithm outperforms the baseline algorithms in terms of effectiveness of the detected communities.

Crohn’s disease (CD) is a complex and heterogeneous condition with no perfect preclinical model or cure. To address this, we explore adult stem cell-derived organoids that retain their tissue identity and disease-driving traits. We prospectively create a biobank of CD patient-derived organoid cultures (PDOs) from colonic biopsies of 53 subjects across all clinical subtypes and healthy subjects. Gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and identified two major molecular subtypes: immune-deficient infectious CD (IDICD) and stress and senescence-induced fibrostenotic CD (S2FCD). Each subtype shows internal consistency in the transcriptome, genome, and phenome. The spectrum of morphometric, phenotypic, and functional changes within the “living biobank” reveals distinct differences between the molecular subtypes. Drug screens reverse subtype-specific phenotypes, suggesting phenotyped-genotyped CD PDOs can bridge basic biology and patient trials by enabling preclinical phase “0” human trials for personalized therapeutics.

Background: Children participating in the Integrated Child Development Service (ICDS) in India have high rates of iron and vitamin A deficiency. Objective: The objective was to assess the efficacy of a premix fortified with iron and vitamin A and added at the community level to prepared khichdi, a rice and dal mixture, in increasing iron and vitamin A stores and decreasing the prevalence of iron deficiency, anemia, and vitamin A deficiency. Design: This cluster, randomized, double-blind, controlled trial was initiated in 30 Anganwadi centers (daycare centers) in West Bengal state, India. Children aged 36-66 mo (n = 516) attending village-based ICDS centers were randomly assigned to receive either a fortified or a nonfortified premix for 24 wk. Blood was drawn at 0 and 24 wk by venipuncture for the measurement of hemoglobin, serum ferritim and serum retinol. Results: The change in the hemoglobin concentration of anemic children was significantly different between fortified and nonfortified khichdi groups (P < 0.001). Prevalence rates of anemia, iron deficiency, and iron deficiency anemia were significantly lower after 24 wk in the fortified-khichdi group than in the nonfortified-khichdi group (P < 0.001). There were no significant differences in serum retinol concentrations or in the prevalence of vitamin A deficiency between the fortified- and nonfortified-khichdi groups. Conclusion: A premix fortified with iron, vitamin A, and folic acid and added to supplementary food at the community level can be effective at increasing iron stores and reducing the prevalence of iron deficiency and anemia. KEY WORDS Iron deficiency, vitamin A deficiency, fortification, anemia, India, children

Information exchange among individuals is one of the key factors leading to formation of modular structures in social networks, often referred as communities. In this paper, we devise a novel information diffusion based approach to leverage the latent information exchange among the individuals for identifying communities. Designed an algorithm called PraSar, which has mainly two phases namely seeding and unification. In seeding phase, closely connected groups of nodes called seed communities are identified by analyzing the cascades obtained during information diffusion. In unification phase, the external connections of seed communities are reduced by unifying two or more seed communities. Involvement of cascade that are formed during the diffusion process enables PraSar to operate locally and giving an overall complexity of O (n 2). The theoretical foundation of the proposed approach is established by various theorems. Empirical results on diverse real world datasets are evident for the effectiveness and competitiveness of the PraSar algorithm over state-of-the-art community detection algorithms. • A new community detection algorithm based on cascading is proposed. • Seed communities generated subsequently with cascading. • Novel properties proposed to address monster community formation and over-partitioning. • Experimental results show that the algorithm performs well on diverse networks. [ABSTRACT FROM AUTHOR]

Virulent infectious agents such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and methicillin-resistant Staphylococcus aureus(MRSA) induce tissue damage that recruits neutrophils, monocyte, and macrophages, leading to T cell exhaustion, fibrosis, vascular leak, epithelial cell depletion, and fatal organ damage. Neutrophils, monocytes, and macrophages recruited to pathogen-infected lungs, including SARS-CoV-2–infected lungs, express phosphatidylinositol 3-kinase gamma (PI3Kγ), a signaling protein that coordinates both granulocyte and monocyte trafficking to diseased tissues and immune-suppressive, profibrotic transcription in myeloid cells. PI3Kγ deletion and inhibition with the clinical PI3Kγ inhibitor eganelisib promoted survival in models of infectious diseases, including SARS-CoV-2 and MRSA, by suppressing inflammation, vascular leak, organ damage, and cytokine storm. These results demonstrate essential roles for PI3Kγ in inflammatory lung disease and support the potential use of PI3Kγ inhibitors to suppress inflammation in severe infectious diseases.

ObjectiveTuft cells residing in the intestinal epithelium have diverse functions. In the small intestine, they provide protection against inflammation, combat against helminth and protist infections, and serve as entry portals for enteroviruses. In the colon, they had been implicated in tumourigenesis. Commitment of intestinal progenitor cells to the tuft cell lineage requires Rho GTPase Cell Division Cycle 42 (CDC42), a Rho GTPase that acts downstream of the epidermal growth factor receptor and wingless-related integration site signalling cascades, and the master transcription factor POU class 2 homeobox 3 (POU2F3). This study investigates how this pathway is regulated by the DEAD box containing RNA binding protein DDX5 in vivo.DesignWe assessed the role of DDX5 in tuft cell specification and function in control and epithelial cell-specific Ddx5knockout mice (DDX5ΔIEC) using transcriptomic approaches.ResultsDDX5ΔIECmice harboured a loss of intestinal tuft cell populations, modified microbial repertoire, and altered susceptibilities to ileal inflammation and colonic tumourigenesis. Mechanistically, DDX5 promotes CDC42 protein synthesis through a post-transcriptional mechanism to license tuft cell specification. Importantly, the DDX5-CDC42 axis is parallel but distinct from the known interleukin-13 circuit implicated in tuft cell hyperplasia, and both pathways augment Pou2f3expression in secretory lineage progenitors. In mature tuft cells, DDX5 not only promotes integrin signalling and microbial responses, it also represses gene programmes involved in membrane transport and lipid metabolism.ConclusionRNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.

Key message: In this manuscript, we show that Oryza sativaindica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Abstract: Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position. Previous reports have implicated this protein in viral resistance as well as in gametogenesis, likely through its competition with AGO1 clade members for micro(mi)RNAs and other small (s)RNAs. Although expression of rice AGO18 in specific stages of male gametogenesis has been documented, its major functions in plant development remain poorly understood. Here, we show that Oryza sativa indicaAGO18 is involved in male gametophyte development. Knockdown (KD) of AGO18 in transgenic rice lines resulted in stunted plants that are male sterile, whereas their carpels were functional. Transcriptome analysis revealed downregulation of several pollen development-associated genes in KD lines. sRNA sequencing in vegetative and reproductive tissues of KD lines indicated reduction of miRNAs and phased secondary sRNAs implicated in male gametophyte development. Our results indicate a distinct role for rice AGO18 in male fertility.

ABSTRACTMicrobial sensors play an essential role in maintaining cellular homoeostasis. Our knowledge is limited on how microbial sensing helps in differential immune response and its link to inflammatory diseases. Recently we have confirmed that ELMO1 (Engulfment and Cell Motility Protein-1) present in cytosol is involved in pathogen sensing, engulfment, and intestinal inflammation. Here, we show that ELMO1 interacts with another sensor, NOD2 (Nucleotide-binding oligomerization domain-containing protein 2), that recognizes bacterial cell wall component muramyl dipeptide (MDP). The polymorphism of NOD2 is linked to Crohn’s disease (CD) pathogenesis. Interestingly, we found that overexpression of ELMO1 and mutant NOD2 (L1007fs) were not able to clear the CD-associated adherent invasive E. coli (AIEC-LF82). The functional implications of ELMO1-NOD2 interaction in epithelial cells were evaluated by using enteroid-derived monolayers (EDMs) from ELMO1 and NOD2 KO mice. Subsequently we also assessed the immune response in J774 macrophages depleted of either ELMO1 or NOD2 or both. The infection of murine EDMs with AIEC-LF82 showed higher bacterial load in ELMO1-KO, NOD2 KO EDMs, and ELMO1 KO EDMs treated with NOD2 inhibitors. The murine macrophage cells showed that the downregulation of ELMO1 and NOD2 is associated with impaired bacterial clearance that is linked to reduce pro-inflammatory cytokines and reactive oxygen species. Our results indicated that the crosstalk between microbial sensors in enteric infection and inflammatory diseases impacts the fate of the bacterial load and disease pathogenesis.

A study using a multi-organoid platform and state-of-the-art transcriptional profiling identifies potential therapeutic targets against SARS-CoV-2. The authors find that CIART, a gene involved in circadian regulation, promotes SARS-CoV-2 infection by regulating the retinoid X receptor pathway and fatty acid synthesis.

During Helicobacter pylori infection, T cells are recruited to the gastric mucosa, but the host T-cell response is not sufficient to clear the infection. Some of the recruited T cells respond in a polarized manner to a Th1 response, while others become anergic. We have previously shown that T-cell anergy may be induced during infection by the interaction of T cells with B7-H1, which is up-regulated on the gastric epithelium during H. pylori infection. Recently, regulatory T (Treg) cells with a CD4+CD25highFoxP3+phenotype were found at an increased frequency in the gastric mucosa of biopsy specimens from H. pylori-infected patients. While Treg cells are important in maintaining tolerance, they can also suppress immune responses during infection. In this study, we examined the induction of the Treg phenotype when naïve T cells were incubated with gastric epithelial cells exposed to H. pylori. The frequency of this phenotype was markedly decreased when B7-H1 was blocked with monoclonal antibodies or its expression was blocked with small interfering RNA. The functional role of these Treg cells was assessed in proliferation assays when the cells were cocultured with activated T cells, which effectively decreased proliferation of the cells.

ABSTRACTDuring Helicobacter pyloriinfection, T cells are recruited to the gastric mucosa, but the host T-cell response is not sufficient to clear the infection. Some of the recruited T cells respond in a polarized manner to a Th1 response, while others become anergic. We have previously shown that T-cell anergy may be induced during infection by the interaction of T cells with B7-H1, which is up-regulated on the gastric epithelium during H. pyloriinfection. Recently, regulatory T (Treg) cells with a CD4+CD25highFoxP3+phenotype were found at an increased frequency in the gastric mucosa of biopsy specimens from H. pylori-infected patients. While Treg cells are important in maintaining tolerance, they can also suppress immune responses during infection. In this study, we examined the induction of the Treg phenotype when naïve T cells were incubated with gastric epithelial cells exposed to H. pylori. The frequency of this phenotype was markedly decreased when B7-H1 was blocked with monoclonal antibodies or its expression was blocked with small interfering RNA. The functional role of these Treg cells was assessed in proliferation assays when the cells were cocultured with activated T cells, which effectively decreased proliferation of the cells.

Comparison of global transcription profiles of Vibrio choleraegrown in vitro and in vivo revealed that 20% of the genome was repressed and about 5% was induced under in vivo conditions. Hybridization with the cloned genes revealed that the virulence genes ctx, toxR, toxT and tcpA were induced under in vivo conditions. Dissection of two in vivo induced cosmids identified another set of three genes homologous to cheY1involved in motility and chemotaxis, pnuC encoding the major component of the nicotinamide mononucleotide transport system and icmFbelonging to a cassette involved in multiplication inside host cells. These results demonstrate that the global transcription profile approach might be a powerful method for identification of differentially expressed transcripts under in vivo conditions.

ABSTRACTEvidence suggests that a repertoire of Vibrio choleraegenes are differentially expressed in vivo, and regulation of virulence factors in vivo may follow a different pathway. Our work was aimed at characterization of in vivo-grown bacteria and identification of genes that are differentially expressed following infection by RNA arbitrarily primed (RAP)-PCR fingerprinting. The ligated rabbit ileal loop model was used. The motility of in vivo-grown bacteria increased by 350% over that of in vitro-grown bacteria. Also, the in vivo-grown cells were more resistant to killing by human serum. By using the RAP-PCR strategy, five differentially expressed transcripts were identified. Two in vitro-induced transcripts encoded polypeptides for the leucine tRNA synthatase and the 50S ribosomal protein, and the three in vivo-induced transcripts encoded the SucA and MurE proteins and a polypeptide of unknown function. MurE is a protein involved in the peptidoglycan biosynthetic pathway. The lytic profiles of in vivo- and in vitro-grown cells suspended in distilled water were compared; the former was found to be slightly less sensitive to lysis. Ultrathin sections of both cells observed under the transmission electron microscope revealed that in contrast to the usual wavy discontinuous membrane structure of the in vitro-grown cells, in vivo-grown cells had a more rigid, clearly visible double-layered structure. The V. cholerae murEgene was cloned and sequenced. The sequence contained an open reading frame of 1,488 nucleotides with its own ribosome-binding site. A plasmid containing the murEgene of V. choleraewas transformed into V. cholerae569B, and a transformed strain, 569BME, containing the plasmid was obtained. Ultrathin sections of 569BME viewed under a transmission electron microscope revealed a slightly more rigid cell wall than that of wild-type 569B. When V. cholerae569B and 569BME cells were injected separately into ligated rabbit ileal loops, the transformed cells had a preference for growth in the ileal loops versus laboratory conditions.

Here, we describe the use of polarized patient enteroid-derived monolayers (EDMs) to assess the impact of e-cigarettes on the human gut barrier. These EDMs can be adapted to culture in a 96-well plate for high-throughput screening. We model the effect of e-cigarettes by combining pathogens, enteroids, and e-cigarette vapor-infused media and assess gut barrier integrity, bacterial internalization, and inflammatory response of the gut epithelium. This protocol can be used to assess the effects of e-cigarette components on gut functions.

ABSTRACTHost engulfment protein ELMO1 generates intestinal inflammation following internalization of enteric bacteria. In Shigella, bacterial effector IpgB1 interacts with ELMO1 and promotes bacterial invasion. IpgB1 belongs to the WxxxE effector family, a motif found in several effectors of enteric pathogens. Here, we have studied the role of WxxxE effectors, with emphasis on SalmonellaSifA and whether it interacts with ELMO1 to regulate inflammation. In-silico-analysis of WxxxE effectors was performed using BLAST search and Clustal W program. The interaction of ELMO1 with SifA was assessed by GST pulldown assay and co-immunoprecipitation. ELMO1 knockout mice, and ELMO1-depleted murine macrophage J774 cell lines were challenged with WT and SifAmutant Salmonella. Bacterial effectors containing the WxxxE motif were transfected in WT and ELMO1-depleted J774 cells to assess the inflammatory cytokines. ELMO1 generates differential pro-inflammatory cytokines between pathogenic and nonpathogenic bacteria. WxxxE motif is present in pathogens and in the TIR domain of host proteins. The C-terminal part of ELMO1 interacts with SifA where WxxxE motif is important for interaction. ELMO1–SifA interaction affects bacterial colonization, dissemination, and inflammatory cytokines in vivo. Moreover, ELMO1–SifA interaction increases TNF-α and IL-6 production from the macrophage cell line and is associated with enhanced Rac1 activity. ELMO1 also interacts with WxxxE effectors IpgB1, IpgB2, and Map and induces inflammation after challenge with microbes or microbial ligands. ELMO1 generates a differential response through interaction with the WxxxE motif, which is absent in commensals. ELMO1-WxxxE interaction plays a role in bacterial pathogenesis and induction of inflammatory response.

Comparison of global transcription profiles of Vibrio cholerae grown in vitro and in vivo revealed that 20% of the genome was repressed and about 5% was induced under in vivo conditions. Hybridization with the cloned genes revealed that the virulence genes ctx, toxR, toxT and tcpA were induced under in vivo conditions. Dissection of two in vivo induced cosmids identified another set of three genes homologous to cheY1 involved in motility and chemotaxis, pnuC encoding the major component of the nicotinamide mononucleotide transport system and icmF belonging to a cassette involved in multiplication inside host cells. These results demonstrate that the global transcription profile approach might be a powerful method for identification of differentially expressed transcripts under in vivo conditions.