Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.

As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, ß-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.

Phenotypic landscape of a bacterial cell.

The explosion of sequence information in bacteria makes developing high-throughput, cost-effective approaches to matching genes with phenotypes imperative. Using E. coli as proof of principle, we show that combining large-scale chemical genomics with quantitative fitness measurements provides a high-quality data set rich in discovery. Probing growth profiles of a mutant library in hundreds of conditions in parallel yielded > 10,000 phenotypes that allowed us to study gene essentiality, discover leads for gene function and drug action, and understand higher-order organization of the bacterial chromosome. We highlight new information derived from the study, including insights into a gene involved in multiple antibiotic resistance and the synergy between a broadly used combinatory antibiotic therapy, trimethoprim and sulfonamides. This data set, publicly available at http://ecoliwiki.net/tools/chemgen/, is a valuable resource for both the microbiological and bioinformatic communities, as it provides high-confidence associations between hundreds of annotated and uncharacterized genes as well as inferences about the mode of action of several poorly understood drugs.

Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO2 through geologic time should be reevaluated.

The history of Earth's carbon cycle reflects trends in atmospheric composition convolved with the evolution of photosynthesis. Fortunately, key parts of the carbon cycle have been recorded in the carbon isotope ratios of sedimentary rocks. The dominant model used to interpret this record as a proxy for ancient atmospheric CO2 is based on carbon isotope fractionations of modern photoautotrophs, and longstanding questions remain about how their evolution might have impacted the record. Therefore, we measured both biomass (εp) and enzymatic (εRubisco) carbon isotope fractionations of a cyanobacterial strain (Synechococcus elongatus PCC 7942) solely expressing a putative ancestral Form 1B rubisco dating to ≫1 Ga. This strain, nicknamed ANC, grows in ambient pCO2 and displays larger εp values than WT, despite having a much smaller εRubisco (17.23 ± 0.61‰ vs. 25.18 ± 0.31‰, respectively). Surprisingly, ANC εp exceeded ANC εRubisco in all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. Such models can be rectified by introducing additional isotopic fractionation associated with powered inorganic carbon uptake mechanisms present in Cyanobacteria, but this amendment hinders the ability to accurately estimate historical pCO2 from geological data. Understanding the evolution of rubisco and the CO2 concentrating mechanism is therefore critical for interpreting the carbon isotope record, and fluctuations in the record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2.

Regulation of peptidoglycan synthesis by outer-membrane proteins.

Growth of the mesh-like peptidoglycan (PG) sacculus located between the bacterial inner and outer membranes (OM) is tightly regulated to ensure cellular integrity, maintain cell shape, and orchestrate division. Cytoskeletal elements direct placement and activity of PG synthases from inside the cell, but precise spatiotemporal control over this process is poorly understood. We demonstrate that PG synthases are also controlled from outside of the sacculus. Two OM lipoproteins, LpoA and LpoB, are essential for the function, respectively, of PBP1A and PBP1B, the major E. coli bifunctional PG synthases. Each Lpo protein binds specifically to its cognate PBP and stimulates its transpeptidase activity, thereby facilitating attachment of new PG to the sacculus. LpoB shows partial septal localization, and our data suggest that the LpoB-PBP1B complex contributes to OM constriction during cell division. LpoA/LpoB and their PBP-docking regions are restricted to γ-proteobacteria, providing models for niche-specific regulation of sacculus growth.

Early childhood language gains, kindergarten readiness, and Grade 3 reading achievement.

In this preregistered study, we used latent change score models to address two research aims: (1) whether preschool-aged children's language gains, over a year of early childhood education, were associated with later performance on state-mandated, literacy-focused kindergarten readiness and Grade 3 reading achievement assessments, and (2) whether gains in language, a more complex skill, predicted these outcomes after controlling for more basic emergent literacy skills. There were 724 participating children (mean = 57 months; 51% male; 76% White, 12% Black, 6% multiple races, and 5% Hispanic or Latino). We found that language gains significantly predicted kindergarten readiness when estimated in isolation (effect = 0.24 SDs, p < .001), but not when gains in letter knowledge and phonological awareness were also included.

Evaluation of an enhanced depression and anxiety screening with targeted pharmacist intervention.

BACKGROUND: Depression is a major source of morbidity but often goes undiagnosed. Broader screening is recommended, and pharmacists could contribute. OBJECTIVES: This study aimed to assess the feasibility of community pharmacy depression and anxiety screening and describe the medication-related problems (MRPs) identified, pharmacist interventions, and provider responses for high-risk patients. METHODS: This pilot was conducted between October 2022 and January 2023 at an independently owned community pharmacy in the Midwest United States. Patients aged 18-45 years with ready prescriptions were identified through weekly reports, and tags were placed on prescription bags. A convenience sample of patients fluent in English were offered the Patient Health Questionnaire (PHQ2) and Generalized Anxiety Disorder (GAD2), with follow-up PHQ9 and GAD7 for at-risk individuals. High-risk individuals met with the pharmacist for consultation and recommendations were discussed. Descriptive statistics were calculated for participant demographics, questionnaire responses, MRPs, and provider responses. Patient profiles were examined 2 months after the workup to identify medication changes. RESULTS: A total of 29 patients volunteered to be screened for anxiety and depression; of these, 41% scored in the high-risk category for depression or anxiety and met with the pharmacist for the consultation. The pharmacist identified multiple MRPs. The most common was the need for additional therapy and inadequate dosages. Patients were reluctant for the pharmacist to follow up with their prescriber and were unreachable for telephone follow-up. Profiles reviewed 2 months after assessment showed half of the at-risk patients had one or more mental health medication changes. CONCLUSION: Community pharmacists may have a role in the screening and management of patient mental health, although there were challenges with screening uptake and follow-up. The pharmacist identified multiple MRPs for this high-risk group for which greater routine monitoring and follow-up may be beneficial. More work seems needed to engage both patients and prescribers.

Evaluation of an enhanced depression and anxiety screening with targeted pharmacist intervention.

BACKGROUND: Depression is a major source of morbidity but often goes undiagnosed. Broader screening is recommended, and pharmacists could contribute. OBJECTIVES: This study aimed to assess the feasibility of community pharmacy depression and anxiety screening and describe the medication-related problems (MRPs) identified, pharmacist interventions, and provider responses for high-risk patients. METHODS: This pilot was conducted between October 2022 and January 2023 at an independently owned community pharmacy in the Midwest United States. Patients aged 18-45 years with ready prescriptions were identified through weekly reports, and tags were placed on prescription bags. A convenience sample of patients fluent in English were offered the Patient Health Questionnaire (PHQ2) and Generalized Anxiety Disorder (GAD2), with follow-up PHQ9 and GAD7 for at-risk individuals. High-risk individuals met with the pharmacist for consultation and recommendations were discussed. Descriptive statistics were calculated for participant demographics, questionnaire responses, MRPs, and provider responses. Patient profiles were examined 2 months after the workup to identify medication changes. RESULTS: A total of 29 patients volunteered to be screened for anxiety and depression; of these, 41% scored in the high-risk category for depression or anxiety and met with the pharmacist for the consultation. The pharmacist identified multiple MRPs. The most common was the need for additional therapy and inadequate dosages. Patients were reluctant for the pharmacist to follow up with their prescriber and were unreachable for telephone follow-up. Profiles reviewed 2 months after assessment showed half of the at-risk patients had one or more mental health medication changes. CONCLUSION: Community pharmacists may have a role in the screening and management of patient mental health, although there were challenges with screening uptake and follow-up. The pharmacist identified multiple MRPs for this high-risk group for which greater routine monitoring and follow-up may be beneficial. More work seems needed to engage both patients and prescribers.

The neuroprotective N-terminal amyloid-ß core hexapeptide reverses reactive gliosis and gliotoxicity in Alzheimer's disease pathology models.

BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by accumulation of extracellular amyloid beta (Aß) and intracellular neurofibrillary tangles, leading to chronic activation of astrocytes and microglia and persistent neuroinflammation. Aß-linked activation of microglia and astrocytes leads to increased intracellular calcium and production of proinflammatory cytokines, impacting the progression of neurodegeneration. An N-terminal Aß fragment (Aß1-15) and a shorter hexapeptide core sequence within the N-Aß fragment (N-Aßcore: Aß10-15) have previously been shown to protect against Aß-induced mitochondrial dysfunction, oxidative stress and apoptosis in neurons and rescue synaptic and spatial memory deficits in an APP/PSEN1 mouse model. Here, we hypothesized that the N-Aß fragment and N-Aßcore are protective against Aß-induced gliotoxicity, promoting a neuroprotective environment and potentially alleviating the characteristically persistent neuroinflammation present in AD. METHODS: We treated ex vivo organotypic brain slice cultures from an aged familial AD mouse model, 5xFAD, with the N-Aßcore and used immunocytochemistry to assess the impact on astrogliosis and microgliosis and alterations in synaptophysin-positive puncta engulfed by microglia. Isolated neuron/glia cultures, mixed glial cultures or a microglial cell line were treated with oligomeric human Aß at concentrations mimicking the pathogenic concentrations (µM) observed in AD in the absence or presence of the non-toxic N-terminal Aß fragments. Resultant changes in synaptic density, gliosis, oxidative stress, mitochondrial dysfunction, apoptosis, and the expression and release of proinflammatory markers were then determined. RESULTS: We demonstrate that the N-terminal Aß fragments mitigated the phenotypic switch leading to astrogliosis and microgliosis induced by pathological concentrations of Aß in mixed glial cultures and organotypic brain slice cultures from the transgenic 5xFAD mouse model, while protecting against Aß-induced oxidative stress, mitochondrial dysfunction and apoptosis in isolated astrocytes and microglia. Moreover, the addition of the N-Aßcore attenuated the expression and release of proinflammatory mediators in microglial cells activated by Aß and rescued microglia-mediated loss of synaptic elements induced by pathological levels of Aß. CONCLUSIONS: Together, these findings indicate the protective functions of the N-terminal Aß fragments extend to reactive gliosis and gliotoxicity induced by Aß, by preventing or reversing glial reactive states indicative of neuroinflammation and synaptic loss central to AD pathogenesis.

Hepatitis C screening in a community pharmacy setting: Patient perspective.

BACKGROUND: Hepatitis C virus (HCV) is an infection of the liver, which contributes to over 15,000 deaths in the United States annually. When treated, HCV has a 90% or greater cure rate, however testing for HCV remains low. OBJECTIVES: To assess patient perspectives on HCV screenings in the community pharmacy setting including awareness of screening, willingness to be screened, barriers to screening, and willingness to pay for HCV screening. METHODS: This study used a cross-sectional survey design. The surveys were distributed by staff at an independent community pharmacy participating in an HCV screening initiative through the state department of public health. Eligible patients were born between 1945 and 1965. Descriptive statistics were calculated for survey variables. Open-ended responses were analyzed for additional context. RESULTS: Fifty-seven surveys were returned and analyzed. The majority of the respondents were White (94%), female (56%), and had some college education (26%). Only 7% were aware that a finger-stick point-of-care test was available and 67% were unaware of the Centers for Disease Control and Prevention (CDC) recommendation for testing. The most frequently reported barrier or hesitation to screening was the patient not thinking they were at risk (29%) followed by uncertainty about cost (14%). Over half of respondents (63%) were either somewhat interested or very interested in testing in a community pharmacy, however, the majority (71%) were not willing to pay or only willing to pay less than $20. CONCLUSIONS: Survey respondents were largely unaware of the recommendations and availability of finger-stick HCV screenings at community pharmacies but many were willing to be tested if low-cost. Providing patient education on the importance of HCV screenings and CDC recommendations may bolster interest in screening.

Selective coactivation of α7- and α4ß2-nicotinic acetylcholine receptors reverses beta-amyloid-induced synaptic dysfunction.

Beta-amyloid (Aß) has been recognized as an early trigger in the pathogenesis of Alzheimer's disease (AD) leading to synaptic and cognitive impairments. Aß can alter neuronal signaling through interactions with nicotinic acetylcholine receptors (nAChRs), contributing to synaptic dysfunction in AD. The three major nAChR subtypes in the hippocampus are composed of α7-, α4ß2-, and α3ß4-nAChRs. Aß selectively affects α7- and α4ß2-nAChRs, but not α3ß4-nAChRs in hippocampal neurons, resulting in neuronal hyperexcitation. However, how nAChR subtype selectivity for Aß affects synaptic function in AD is not completely understood. Here, we showed that Aß associated with α7- and α4ß2-nAChRs but not α3ß4-nAChRs. Computational modeling suggested that two amino acids in α7-nAChRs, arginine 208 and glutamate 211, were important for the interaction between Aß and α7-containing nAChRs. These residues are conserved only in the α7 and α4 subunits. We therefore mutated these amino acids in α7-containing nAChRs to mimic the α3 subunit and found that mutant α7-containing receptors were unable to interact with Aß. In addition, mutant α3-containing nAChRs mimicking the α7 subunit interact with Aß. This provides direct molecular evidence for how Aß selectively interacted with α7- and α4ß2-nAChRs, but not α3ß4-nAChRs. Selective coactivation of α7- and α4ß2-nAChRs also sufficiently reversed Aß-induced AMPA receptor dysfunction, including Aß-induced reduction of AMPA receptor phosphorylation and surface expression in hippocampal neurons. Moreover, costimulation of α7- and α4ß2-nAChRs reversed the Aß-induced disruption of long-term potentiation. These findings support a novel mechanism for Aß's impact on synaptic function in AD, namely, the differential regulation of nAChR subtypes.

Small RNA and degradome deep sequencing reveals important roles of microRNAs in cotton (Gossypium hirsutum L.) response to root-knot nematode Meloidogyne incognita infection.

Investigation of cotton response to nematode infection will allow us to better understand the cotton immune defense mechanism and design a better biotechnological approach for efficiently managing pest nematodes in cotton. In this study, we firstly treated cotton by root knot nematode (RKN, Meloidogyne incognita) infections, then we employed the high throughput deep sequencing technology to sequence and genome-widely identify all miRNAs in cotton; finally, we analyzed the functions of these miRNAs in cotton response to RKN infections. A total of 266 miRNAs, including 193 known and 73 novel miRNAs, were identified by deep sequencing technology, which belong to 67 conserved and 66 novel miRNA families, respectively. A majority of identified miRNA families only contain one miRNA; however, miR482 family contains 14 members and some others contain 2-13 members. Certain miRNAs were specifically expressed in RKN-infected cotton roots and others were completely inhibited by RKN infection. A total of 50 miRNAs were differentially expressed after RKN infection, in which 28 miRNAs were up-regulated and 22 were inhibited by RKN treatment. Based on degradome sequencing, 87 gene targets were identified to be targeted by 57 miRNAs. These miRNA-targeted genes are involved in the interaction of cotton plants and nematode infection. Based on GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, 466 genes from all 636 miRNA targets were mapped to 6340 GO terms, 181 genes from 228 targets of differentially expressed miRNAs were mapped to 1588 GO terms. The GO terms were then categorized into the three main GO classes: biological processes, cellular components, and molecular functions. The targets of differentially expressed miRNAs were enriched in 43 GO terms, including 22 biological processes, 10 cellular components, and 11 molecular functions (p < 0.05). Many identified processes were associated with organism responses to the environmental stresses, including regulation of nematode larval development, response to nematode, and response to flooding. Our results will enhance the study and application of developing new cotton cultivars for nematode resistance.

The relationship between the gut microbiome and host gene expression: a review.

Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.

A nonproteinaceous Fusarium cell wall extract triggers receptor-like protein-dependent immune responses in Arabidopsis and cotton.

Fusarium wilt caused by the ascomycete fungus Fusarium oxysporum is a devastating disease of many economically important crops. The mechanisms underlying plant responses to F. oxysporum infections remain largely unknown. We demonstrate here that a water-soluble, heat-resistant and nonproteinaceous F. oxysporum cell wall extract (FoCWE) component from multiple F. oxysporum isolates functions as a race-nonspecific elicitor, also termed pathogen-associated molecular pattern (PAMP). FoCWE triggers several demonstrated immune responses, including mitogen-activated protein (MAP) kinase phosphorylation, reactive oxygen species (ROS) burst, ethylene production, and stomatal closure, in cotton and Arabidopsis. Pretreated FoCWE protects cotton seeds against infections by virulent F. oxysporum f. sp. vasinfectum (Fov), and Arabidopsis plants against the virulent bacterium, Pseudomonas syringae, suggesting the potential application of FoCWEs in crop protection. Host-mediated responses to FoCWE do not appear to require LYKs/CERK1, BAK1 or SOBIR1, which are commonly involved in PAMP perception and/or signalling. However, FoCWE responses and Fusarium resistance in cotton partially require two receptor-like proteins, GhRLP20 and GhRLP31. Transcriptome analysis suggests that FoCWE preferentially activates cell wall-mediated defence, and Fov has evolved virulence mechanisms to suppress FoCWE-induced defence. These findings suggest that FoCWE is a classical PAMP that is potentially recognised by a novel pattern-recognition receptor to regulate cotton resistance to Fusarium infections.

Detection and Characterization of Fusarium Wilt (Fusarium oxysporum f. sp. vasinfectum) Race 4 Causing Fusarium Wilt of Cotton Seedlings in New Mexico.

Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. vasinfectum (Atk.) W.C. Snyder & H.N. Hans (FOV), is one of the most destructive diseases of cotton (Gossypium spp.) worldwide. FOV race 4 (FOV4) is a highly virulent nominal race of this pathogen and a significant threat to cotton production in the western and southwestern USA and, potentially, the entire Cotton Belt. A field survey to identify FOV4 was performed in three southern counties of New Mexico in 619 cotton fields from 2018 to 2020. From 132 samples of cotton plants that exhibited wilt symptoms, Fusarium spp. were the most frequently isolated group of fungal species, with an isolation frequency of 57.4%. Eighty-four Fusarium spp. isolates were subsequently characterized by a DNA sequence analysis of three genes, EF-1α, PHO, and BT, encoding for translation elongation factor, phosphate permease, and ß-tubulin, respectively. Forty-two isolates from 10 cotton fields were identified as FOV4 and confirmed with a positive 500-bp fragment diagnostic for FOV4. Twenty-six (62%) of the 42 FOV4 isolates were T type and the remainder (38%) were null type with and without a Tfo1 insertion in PHO, respectively. Each FOV4-infested field contained the same FOV4 genotype. Ten representative FOV4 isolates (one each from the 10 FOV4-infested fields) were evaluated for their pathogenicity on resistant Pima PHY 841 RF and susceptible Upland PHY 725 RF at 7, 14, 21, and 28 days after inoculation under temperature-controlled conditions at 21 to 22°C. Based on the disease severity rating, mortality rate, and area under the disease progress curve value, all 10 isolates were pathogenic to both cotton cultivars and differed in virulence; four isolates of the T genotype as a whole were more virulent than the six isolates of the N genotype. PHY 841 RF had significantly higher levels of resistance than PHY 725 RF to all FOV4 isolates. The results provide the first comprehensive account of the occurrence, distribution, and virulence of FOV4 in cotton production in New Mexico and will be useful for developing an effective strategy to manage FW in the state of New Mexico and the entire western and southwestern Cotton Belt.

Characterization of Current Fusarium oxysporum f. sp. vasinfectum Isolates from Cotton in the San Joaquin Valley of California and Lower Valley El Paso, Texas.

Fusarium oxysporum f. sp. vasinfectum race 4 is a causal agent of Fusarium wilt of cotton (Gossypium spp.). This study aimed to characterize the existing distribution and frequency of current field populations of F. oxysporum f. sp. vasinfectum race 4 genotypes in the San Joaquin Valley (SJV) of California and Lower Valley El Paso, TX and examine representative isolates for aggressiveness during different stages of seedling development. A survey was conducted from 2017 to 2019 across 13 locations in the SJV and one location in El Paso, TX during 2018. From the SJV, isolates identified as the F. oxysporum f. sp. vasinfectum race 4 T genotype were dispersed across the SJV, whereas isolates identified as the F. oxysporum f. sp. vasinfectum race 4 N genotype were most frequently isolated from cotton fields in the northern county of Merced. The F. oxysporum f. sp. vasinfectum race 4 isolates from the Texas location were identified as the MT genotype. A selection of representative isolates was evaluated using three inoculation assays (rolled-towel, F. oxysporum f. sp. vasinfectum-infested oat seed, and root-dip inoculation) to test the isolates' abilities to produce symptoms during seedling stages of cotton development. All isolates tested were capable of producing symptoms on cotton; however, isolate aggressiveness varied within and across inoculation assays. In all assays, higher levels of disease development were observed in the moderately susceptible Pima (Gossypium barbadense L.) cultivars (DP-340 or PHY-830) when compared with the moderately tolerant Upland (G. hirsutum L.) cultivar (FM-2334). However, no correlation was found among the different response variables for the rolled-towel assay when compared with the root-dip and infested oat seed assays. These results suggest that different genes are involved in the resistance response during the early seedling development stage measured in the rolled-towel assay compared with the later seedling development stages measured during the root-dip inoculation and infested oat seed assays, revealing the complexity of the Fusarium wilt disease and host-plant resistance mechanisms.

Interplay Between the Host, the Human Microbiome, and Drug Metabolism.

The human microbiome is composed of four major areas including intestinal, skin, vaginal, and oral microbiomes, with each area containing unique species and unique functionalities. The human microbiome may be modulated with prebiotics, probiotics, and postbiotics to potentially aid in the treatment of diseases like irritable bowel syndrome, bacterial vaginosis, atopic dermatitis, gingivitis, obesity, or cancer. There is also potential for many of the inhabitants of the human microbiome to directly modulate host gene expression and modulate host detoxifying enzyme activity like cytochrome P450s (CYPs), dehydrogenases, and carboxylesterases. Therefore, the microbiome may be important to consider during drug discovery, risk assessment, and dosing regimens for various diseases given that the human microbiome has been shown to impact host detoxification processes.

Characterization of the Complete Genome and P0 Protein for a Previously Unreported Genotype of Cotton Leafroll Dwarf Virus, an Introduced Polerovirus in the United States.

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

MicroRNA-target gene responses to root knot nematode (Meloidogyne incognita) infection in cotton (Gossypium hirsutum L.).

MicroRNAs (miRNAs) are a large class of small regulatory RNA molecules, however no study has been performed to elucidate the role of miRNAs in cotton (Gossypium hirsutum) response to the root knot nematode (RKN, Meloidogyne incognita) infection. We selected 28 miRNAs and 8 miRNA target genes to investigate the miRNA-target gene response to M. incognita infection. Our results show that RKN infection significantly affected the expression of several miRNAs and their targeted genes. After 10 days of RKN infection, expression fold changes on miRNA expressions ranged from down-regulated by 33% to upregulated by 406%; meanwhile the expression levels of miRNA target genes were 45.8% to 231%. Three miRNA-target pairs, miR159-MYB, miR319-TCP4 and miR167-ARF8, showed inverse expression patterns between gene targets and their corresponded miRNAs, suggesting miRNA-mediated gene regulation in cotton roots in response to RKN infection.

The effect of two QTLs for resistance to Meloidogyne incognita in cotton on nematode egression from roots.

Cotton is widely grown in the southern US and Meloidogyne incognita is its most significant pathogen. The germplasm line M-120 RNR is highly resistant to M. incognita due to two resistance QTLs (quantitative trait loci), qMi-C11 and qMi-C14. Both QTLs reduce total egg production, but the QTLs affect M. incognita development at different life stages. The QTLs do not appear to affect initial penetration of M. incognita but genotypes containing qMi-C11 had fewer nematodes in the roots 8 days after inoculation than near isolines without qMi-C11, which may indicate M. incognita egression from roots. Three greenhouse trials were conducted using cotton isolines to determine whether qMi-C11 and qMi-C14 affect egression of M. incognita juveniles from roots. On each of the five sampling dates (4, 6, 8, 10, and 12 DAI), nematodes that egressed from roots were counted and roots were stained to count nematodes that remained in the roots. The effect of resistance QTLs on M. incognita egression from the roots differed among the trials. Nematode egression was consistently numerically greater, but inconsistently statistically different, from plants with both QTLs than from plants with neither QTL. Plants with only one QTL generally did not differ from plants with both QTLs, and the effects of qMi-C11 and qMi-C14 did not differ in any consistent way. In a separate experiment, plants with neither QTL had more eggs per egg mass than did plants with both QTLs, whereas plants with only one QTL had an intermediate number. Root gall size was measured in two trials and no consistent differences in gall size were observed. We conclude that (1) qMi-C11 and qMi-C14 do not stimulate nematode egression from cotton roots, (2) both qMi-C11 and qMi-C14 reduce M. incognita eggs/egg mass, and (3) neither qMi-C11 nor qMi-C14 affect gall size.

Encapsulins: molecular biology of the shell.

Compartmentalization is both a fundamental principle of cellular organization and an emerging theme in prokaryotic biology. Work in the past few decades has shown that protein-based organelles called microcompartments enhance the function of encapsulated cargo proteins. More recently, the repertoire of known prokaryotic organelles has expanded beyond microcompartments to include a new class of smaller proteinaceous compartments, termed nanocompartments (also known as encapsulins). Nanocompartments are icosahedral capsids that are smaller and less complex than microcompartments. Encapsulins are formed by a single species of shell protein that self-assembles and typically encapsulates only one type of cargo protein. Significant progress has been made in understanding the structure of nanocompartment shells and the loading of cargo to the interior. Recent analysis has also demonstrated the prevalence of encapsulin genes throughout prokaryotic genomes and documented a large diversity of cargo proteins with a variety of novel functions, suggesting that nanocompartments play an important role in many microbes. Here we review the current understanding of encapsulin structure and function and highlight exciting open questions of physiological significance.