Abundance In Response Research Articles

Interannual response of euphausiid community abundance during the anomalous warming period (2014–2016) in the Gulf of California

El Niño in the northeast Pacific and Gulf of California typically causes a decrease in euphausiid abundance (biomass), and modifies their latitudinal biogeographic distributions, but the effect of recent marine heat waves (or their combined effect with El Niño) are less understood. The interannual response of euphausiid community structure and abundance were investigated during the cold–warm transition period (June) of six years (2013–2019, except 2015) in the central Gulf of California, Mexico. Abundance in June 2013–2019 was compared with historical baseline for euphausiid abundance made in June 1957 from a California Cooperative Oceanic Fisheries Investigation cruise, just before El Niño 1957–1958. During 2014–2019 two anomalously warm events occurred: the marine heat wave of 2014 (MHW 2014) and El Niño 2015–2016 (May 2015–May 2016). We tested the hypothesis that the numerically dominant subtropical neritic species Nyctiphanes simplex and temperate oceanic Nematoscelis difficilis significantly decrease in abundance in response to the prolonged warming that occurred during 2014–2016 and that tropical euphausiid species could increase in relative abundance during this period. Ten euphausiid species were collected accounting for < 3% of total relative abundance of 34 zooplankton taxonomic groups collected during June 2013–2014, 2016, 2018 and between 7 and 22.4% during 2017 and 2019. N. simplex and Ne. difficilis accounted for > 80% of euphausiid total abundance during June 2013–2019, with considerably lower abundance during 2013, the MHW 2014, and El Niño 2015–2016 than in June 2017, 2018, and 2019. Mean euphausiid abundance in 2017 and 2019 was slightly higher than that recorded in June 1957. Tropical species increased their relative abundances during El Niño 2015–2016 event, but they were always < 15% of total euphausiid relative abundance during 2013–2019. We estimated that it took at least 3 years for the euphausiid species abundance in the gulf to slowly recover from the unfavorable conditions associated with MHW 2014, and El Niño 2015–2016 to attain highest mean abundance in 2019. Multi–variated ordination analyses showed that the prolonged warming and anomalously low Chl-a concentrations recorded in 2014–2016 negatively influenced euphausiid abundance, a proxy for euphausiid biomass available for pelagic predators in the Gulf of California.

Exploring the interaction between agronomic practices and soil characteristics on the presence of antibiotic resistance genes in soil

In this study, field-scale experiments were carried out to analyze the coupling effects of typical agronomic measures and soil types on soil antibiotic resistance genes (ARGs) using high-throughput fluorescence quantitative PCR. The results indicated that agronomic measures enhanced ARG abundance in different soil types. For the same soil type, the enhancement of ARG abundance in response to agronomic measures could be ordered as follows: livestock manure application (257.6–131.7 %) > sewage irrigation (57.6–35.0 %) > plastic film mulching (21.2–5.0 %). Under the same agronomic measures, enhancement of ARG abundance according to soil type was: clay (257.6–21.2 %) > loam (147.8–15.9 %) > sandy (131.7–5.0 %). Furthermore, the contributions of environmental factors in determining ARG abundance in different soil types differed in response to the application of different agronomic measures. Phthalates had the most and least pronounced effects on ARG abundance in sandy and loam soils, respectively. Effects of moisture on ARG abundance were minor in loam soil, but greater in clay and sandy soils. These findings provide new insights into the dissemination of soil ARGs promoted by the adoption of agronomic measures.

The adaptive response to alternative carbon sources in the pathogen Candida albicans involves a remodeling of thiol- and glutathione-dependent redox status.

Candida albicans is an opportunist pathogen responsible for a large spectrum of infections, from superficial mycosis to systemic diseases known as candidiasis. During infection in vivo, Candida albicans must adapt to host microenvironments and this adaptive response is crucial for the survival of this organism, as it facilitates the effective assimilation of alternative carbon sources others than glucose. We performed a global proteomic analysis on the global changes in protein abundance in response to changes in micronutrient levels, and, in parallel, explored changes in the intracellular redox and metabolic status of the cells. We show here that each of the carbon sources considered - glucose, acetate and lactate - induces a unique pattern of response in C. albicans cells, and that some conditions trigger an original and specific adaptive response involving the adaptation of metabolic pathways, but also a complete remodeling of thiol-dependent antioxidant defenses. Protein S-thiolation and the overproduction of reduced glutathione are two components of the response to high glucose concentration. In the presence of acetate, glutathione-dependent oxidative stress occurs, reduced thiol groups bind to proteins, and glutathione is exported out of the cells, these changes probably being triggered by an increase in glutathione-S-transferases. Overall, our results suggest that the role of cellular redox status regulation and defenses against oxidative stress, including the thiol- and glutathione-dependent response, in the adaptive response of C. albicans to alternative carbon sources should be reconsidered.

Age-dependent nuclear lipid droplet deposition is a cellular hallmark of aging in Caenorhabditis elegans.

Aging is the major risk factor for several life-threatening pathologies and impairs the function of multiple cellular compartments and organelles. Age-dependent deterioration of nuclear morphology is a common feature in evolutionarily divergent organisms. Lipid droplets have been shown to localize in most nuclear compartments, where they impinge on genome architecture and integrity. However, the significance of progressive nuclear lipid accumulation and its impact on organismal homeostasis remain obscure. Here, we implement non-linear imaging modalities to monitor and quantify age-dependent nuclear lipid deposition in Caenorhabditis elegans. We find that lipid droplets increasingly accumulate in the nuclear envelope, during aging. Longevity-promoting interventions, such as low insulin signaling and caloric restriction, abolish the rate of nuclear lipid accrual and decrease the size of lipid droplets. Suppression of lipotoxic lipid accumulation in hypodermal and intestinal nuclei is dependent on the transcription factor HLH-30/TFEB and the triglyceride lipase ATGL-1. HLH-30 regulates the expression of ATGL-1 to reduce nuclear lipid droplet abundance in response to lifespan-extending conditions. Notably, ATGL-1 localizes to the nuclear envelope and moderates lipid content in long-lived mutant nematodes during aging. Our findings indicate that the reduced ATGL-1 activity leads to excessive nuclear lipid accumulation, perturbing nuclear homeostasis and undermining organismal physiology, during aging.

Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies.

The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder PURA Syndrome. PURA binds both DNA and RNA and has been associated with various cellular functions. Only little is known about its main cellular roles and the molecular pathways affected upon PURA depletion. Here, we show that PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Many of these transcripts change abundance in response to PURA depletion. The encoded proteins suggest a role for PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity. Intriguingly, reduced PURA levels decrease the expression of the integral P-body components LSM14A and DDX6 and strongly affect P-body formation in human cells. Furthermore, PURA knockdown results in stabilization of P-body-enriched transcripts, whereas other mRNAs are not affected. Hence, reduced PURA levels, as reported in patients with PURA Syndrome, influence the formation and composition of this phase-separated RNA processing machinery. Our study proposes PURA Syndrome as a new model to study the tight connection between P-body-associated RNA regulation and neurodevelopmental disorders.

Developing the Role of Earth Observation in Spatio-Temporal Mosquito Modelling to Identify Malaria Hot-Spots

Anopheles mosquitoes are the vectors of human malaria, a disease responsible for a significant burden of global disease and over half a million deaths in 2020. Here, methods using a time series of cost-free Earth Observation (EO) data, 45,844 in situ mosquito monitoring captures, and the cloud processing platform Google Earth Engine are developed to identify the biogeographical variables driving the abundance and distribution of three malaria vectors—Anopheles gambiae s.l., An. funestus, and An. paludis—in two highly endemic areas in the Democratic Republic of the Congo. EO-derived topographical and time series land surface temperature and rainfall data sets are analysed using Random Forests (RFs) to identify their relative importance in relation to the abundance of the three mosquito species, and they show how spatial and temporal distributions vary by site, by mosquito species, and by month. The observed relationships differed between species and study areas, with the overall number of biogeographical variables identified as important in relation to species abundance, being 30 for An. gambiae s.l. and An. funestus and 26 for An. paludis. Results indicate rainfall and land surface temperature to consistently be the variables of highest importance, with higher rainfall resulting in greater mosquito abundance through the creation of pools acting as mosquito larval habitats; however, proportional coverage of forest and grassland, as well as proximity to forests, are also consistently identified as important. Predictive application of the RF models generated monthly abundance maps for each species, identifying both spatial and temporal hot-spots of high abundance and, by proxy, increased malaria infection risk. Results indicate greater temporal variability in An. gambiae s.l. and An. paludis abundances in response to seasonal rainfall, whereas An. funestus is generally more temporally stable, with maximum predicted abundances of 122 for An. gambiae s.l., 283 for An. funestus, and 120 for An. paludis. Model validation produced R2 values of 0.717 for An. gambiae s.l., 0.861 for An. funestus, and 0.448 for An. paludis. Monthly abundance values were extracted for 248,089 individual buildings, demonstrating how species abundance, and therefore biting pressure, varies spatially and seasonally on a building-to-building basis. These methods advance previous broader regional mosquito mapping and can provide a crucial tool for designing bespoke control programs and for improving the targeting of resource-constrained disease control activities to reduce malaria transmission and subsequent mortality in endemic regions, in line with the WHO’s ‘High Burden to High Impact’ initiative. The developed method was designed to be widely applicable to other areas, where suitable in situ mosquito monitoring data are available. Training materials were also made freely available in multiple languages, enabling wider uptake and implementation of the methods by users without requiring prior expertise in EO.

Soil arthropod responses to subsoil manuring in irrigated vegetable and rainfed grain production

Diverse soil biology is being increasingly recognised as important for productive soils. Subsoil manuring – the process of placing organic materials underground using a modified deep ripper – has been used to improve the structure and productivity of texture contrast soils. Using soil arthropods as indicator species, this study investigated the soil biology responses of the subsoil manuring approach. Different organic materials were placed in the upper zone of a clay subsoil at field sites used for irrigated vegetable and rainfed grain production. Soil samples were taken from the topsoil and from the depth of organic material placement and processed to extract soil arthropods. Of three suborders of soil arthropods recorded, mesostigmatid mites showed the most notable increases in abundance in response to subsoil manuring. The placement of organic materials at depth resulted in elevated abundance of soil arthropods at depths that are not the normal habitat of these organisms. Abundance and richness were both suppressed under irrigated production compared to rainfed, although it is acknowledged that a number of management practice differences between the two production systems could contribute to the differences observed.

T-cell receptor αβ+ double-negative T cells in the kidney are predominantly extravascular and increase in abundance in response to ischemia-reperfusion injury.

T-cell receptor+ CD4- CD8- double-negative (DN) T cells are a population of T cells present in low abundance in blood and lymphoid organs, but enriched in various organs including the kidney. Despite burgeoning interest in these cells, studies examining their abundance in the kidney have reported conflicting results. Here we developed a flow cytometry strategy to clearly segregate DN T cells from other immune cells in the mouse kidney and used it to characterize their phenotype and response in renal ischemia-reperfusion injury (IRI). These experiments revealed that in the healthy kidney, most DN T cells are located within the renal parenchyma and exhibit an effector memory phenotype. In response to IRI, the number of renal DN T cells is unaltered after 24 h, but significantly increased by 72 h. This increase is not related to alterations in proliferation or apoptosis. By contrast, adoptive transfer studies indicate that circulating DN T cells undergo preferential recruitment to the postischemic kidney. Furthermore, DN T cells show the capacity to upregulate CD8, both invivo following adoptive transfer and in response to exvivo activation. Together, these findings provide novel insights regarding the phenotype of DN T cells in the kidney, including their predominant extravascular location, and show that increases in their abundance in the kidney following IRI occur in part as a result of increased recruitment from the circulation. Furthermore, the observation that DN T cells can upregulate CD8 invivo has important implications for detection and characterization of DN T cells in future studies.

Dynamic Responses of Chromosome-Binding Protein Complexes to Meiotic Prophase I of Mouse Spermatocyte.

Meiotic prophase I (MPI) is the most important event in mammalian meiosis. The status of the chromosome-binding proteins (CBPs) and the corresponding complexes and their functions in MPI have not yet been well scrutinized. Quantitative proteomics focused on MPI-related CBPs was accomplished, in which mouse primary spermatocytes in four different subphases of MPI were collected, and chromosome-enriched proteins were extracted and quantitatively identified. According to a stringent criterion, 1136 CBPs in the MPI subphases were quantified. Looking at the dynamic patterns of CBP abundance in response to MPI progression, the patterns were broadly divided into two groups: high abundance in leptotene and zygotene or that in pachytene and diplotene. Furthermore, 152 such CBPs were regarded as 26 CBP complexes with strict filtration, in which some of these complexes were perceived to be MPI-dependent for the first time. These complexes basically belonged to four functional categories, while their dynamic abundance changes following MPI appeared; the functions of DNA replication decreased; and transcription and synapsis were activated in zygotene, pachytene, and diplotene; in contrast to the traditional prediction, condensin activity weakened in pachytene and diplotene. Profiling of protein complexes thus offered convincing evidence of the importance of CBP complexes in MPI.

Changes in the population and functional profile of bacteria and fungi in the rhizosphere of Suaeda salsa is driven by invasion of Spartina alterniflora

Changes in rhizosphere microbial populations and their functions in response to Spartina alterniflora root invasion could potentially reveal part of the mechanism of Suaeda salsa degradation. In this study, rhizosphere soils were collected from regions where S. alterniflora (SA) and S. salsa (SS) grew independently as well as rhizosphere soil from mixed growth regions (namely MSA and MSS) before applying high-throughput sequencing technology to study the characteristics of microbial communities. The results showed that the physicochemical properties of the rhizosphere soils were different between the groups of samples. However, based on the multi-factor PERMANOVA analysis, only EC and NO3−-N were found to significantly influence the microbial communities’ composition. Furthermore, α diversity indices and β diversity analyses revealed that the diversity and structure of rhizosphere microbial community changed in varying degrees after invasion. Compared with SS, the most abundant bacteria phylum namely Tenericutes, Firmicutes, Proteobacteria and Actinobacteria in MSS were identified as major species that increased significantly in abundance in response to S. alterniflora root invasion, while the composition of fungal community did not change. Furthermore, PICRUSt analysis revealed that the higher abundance of signal transduction, membrane transport, cell motility and certain disease-related functional pathways of MSA and MSS could be conducive to the colonization and survival of bacterial pathogens. Additionally, the analysis of the FUNGuild database confirmed that a higher proportion of pathotroph and pathogen. This could very likely cause S. salsa to be more susceptible to soil pathogenic fungi in mixed growth region. In contrast, the increase of the saprotroph-symbiotroph could be beneficial for the colonization and expansion of S. alterniflora. This study provides a new perspective for elucidating the driving mechanism by microorganisms behind S. salsa’s degradation following S. alterniflora’s invasion.

The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia.

Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia, and short‐term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress‐tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 h of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein‐coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing upregulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia‐by‐habitat of origin or chronic‐by‐acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through upregulation of cuticular proteins and neurotrophins, respectively.

A generically parameterized model of Lake eutrophication: The impact of Stoichiometric ratios and constraints on the abundance of natural phytoplankton communities (GPLake-S)

Water quality improvement to avoid excessive phytoplankton blooms often requires eutrophication management where both phosphorus (P) and nitrogen (N) play a role. While empirical eutrophication studies and ecological resource competition theory both provide insight into phytoplankton abundance in response to nutrient loading, they are not seamlessly linked in the current state of eutrophication research. We argue that understanding species competition for multiple nutrients and light in natural phytoplankton communities is key to assessing phytoplankton abundance under changing nutrient supply. Here we present GPLake-S, a mechanistic model rooted in ecological resource competition theory, which has only eight parameters and can predict chlorophyll-a to nutrient relationships for phytoplankton communities under N, P, N+P colimitation and light limitation. GPLake-S offers a simple mechanistic tool to make first estimates of chlorophyll-a levels and nutrient thresholds for generic lake properties, accounting for variation in N:P ratio preferences of phytoplankton species. This makes the model supportive of water management and policy.

Functional traits and their plasticity shift from tolerant to avoidant under extreme drought.

Under climate change, extreme droughts will limit water availability for plants. However, the species-specific responses make it difficult to draw general conclusions. We hypothesized that changes in species' abundance in response to extreme drought can be best explained by a set of water economic traits under ambient conditions in combination with the ability to adjust these traits towards higher drought resistance. We conducted a 4-year field experiment in temperate grasslands using rainout shelters with 30% and 50% rainfall reduction. We quantified the response as the change in species abundance between ambient conditions and the rainfall reduction. Abundance response to extreme drought was best explained by a combination of traits in ambient conditions and their functional adjustment, most likely reflecting plasticity. Smaller leaved species decreased less in abundance under drought. With increasing drought intensity, we observed a shift from drought tolerance, i.e., an increase in leaf dry matter content, to avoidance, i.e., a less negative turgor loss point (TLP) in ambient conditions and a constancy in TLP under drought. We stress the importance of using a multidimensional approach of variation in multiple traits and the importance of considering a range of drought intensities to improve predictions of species' response to climate change.

Crab bioturbation affects competition between microbial nitrogen removal and retention in estuarine and coastal wetlands

As the important benthic animal in coastal wetlands, crab bioturbation may significantly affect the nitrogen (N) budgets by regulating microbial N transformation processes. However, the response of interaction between different microbial N processes to crab bioturbation remains poorly understood. Here, a 30-day microcosmic experiment was conducted using sediment collected from the Yangtze Estuary wetland, followed by the determination of temporal variations of physicochemical parameters, N removal (denitrification plus anammox, which is defined as N2 production) and retention rates (nitrate dissimilatory reduction to ammonium, DNRA) as well as relevant gene abundances in response to different crabs densities. The results showed that crab bioturbation simultaneously promoted the rates of N2 production and DNRA processes. These two process rates were positively associated with the intensity of crab bioturbation, which was supported by molecular analysis of relevant functional gene abundance. Crab bioturbation was more beneficial to DNRA than N2 production. Due to this disproportionate stimulation, crab bioturbation increased the importance of DNRA, indicating that N retention was becoming more significant under crab bioturbation in estuarine and coastal wetlands. The variations of sediment total organic carbon and oxygen availability driven by crab bioturbation were the critical factors mediating the changes in microbial N removal and retention. Overall, our findings highlighted that crab bioturbation can affect the N budgets in estuarine and coastal wetlands by altering the competition between microbial N removal and retention.

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome

Complex carbohydrates that escape small intestinal digestion, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between microbes and host, resulting in metabolic products that influence host health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. Bacterial species identified as carrying genes encoding starch binding modules increased in abundance in response to starches. The use of hybrid metagenomics has allowed identification of several uncultured species with the functional potential to degrade starch substrates for future study.

Does G Protein-Coupled Estrogen Receptor 1 Contribute to Cisplatin-Induced Acute Kidney Injury in Male Mice?

Nephrotoxicity is the dose-limiting side-effect of the chemotherapeutic agent cisplatin (Cp). Recent evidence points to renal protective actions of G protein-coupled estrogen receptor 1 (GPER1). In addition, it has been shown that GPER1 signaling elicits protective actions against acute ischemic injuries that involve multiple organ systems; however, the involvement of GPER1 signaling in Cp-induced acute kidney injury (AKI) remains unclear. This study tested whether genetic deletion of GPER1 exacerbates Cp-induced AKI in male mice. We subjected male mice, homozygous (homo) and heterozygous (het) knockout for the GPER1 gene, and wild-type (WT) littermates to Cp or saline injections and assessed markers for renal injury on the third day after injections. We also determined serum levels of proinflammatory markers in saline and Cp-treated mice. Given the protective role of heme oxygenase-1 (HO-1) in Cp-mediated apoptosis, we also investigated genotypic differences in renal HO-1 abundance, cell death, and proliferation by Western blotting, the TUNEL assay, and Ki67 immunostaining, respectively. Cp increased serum creatinine, urea, and neutrophil gelatinase-associated lipocalin (NGAL) levels, the renal abundance of kidney injury molecule-1, and NGAL in all groups. Cp-induced AKI resulted in comparable histological evidence of injury in all genotypes. WT and homo mice showed greater renal HO-1 abundance in response to Cp. Renal HO-1 abundance was lower in Cp-treated homo, compared to Cp-treated WT mice. Of note, GPER1 deletion elicited a remarkable increase in renal apoptosis; however, no genotypic differences in cell proliferation were observed. Cp augmented kidney Ki67-positive counts, regardless of the genotype. Overall, our data do not support a role for GPER1 in mediating Cp-induced renal injury. GPER1 deletion promotes renal apoptosis and diminishes HO-1 induction in response to Cp, suggesting that GPER1 may play cytoprotective and anti-apoptotic actions in AKI. GPER1-induced regulation of HO-1 and apoptosis may offer novel therapeutic targets for the treatment of AKI.

Solar radiation and soil moisture drive tropical forest understory responses to experimental and natural hurricanes

AbstractTropical forest understory regeneration occurs rapidly after disturbance with compositional trajectories that depend on species availability and environmental conditions. To predict future tropical forest regeneration dynamics, we need a deeper understanding of how pulse disturbance events, like hurricanes, interact with environmental variability to affect understory demography and composition. We examined fern and sapling mortality, recruitment, and community composition in relation to solar radiation and soil moisture using 17 years of forest dynamics data (2003–2019) from the Canopy Trimming Experiment in the Luquillo Experimental Forest, Puerto Rico. Solar radiation increased 150% and soil moisture increased 40% following canopy trimming of experimental plots relative to control plots. All plots were disturbed in 2017 by Hurricanes Irma and Maria, so experimentally trimmed plots presented the opportunity to study the effects of multiple hurricanes, while control plots isolated the effects of a single natural hurricane. Recruitment rates maximized at 0.14 individuals/plot/month for ferns and 0.20 stems/plot/month for saplings. Recruitment and mortality were distributed more evenly over the 17 years of monitoring in experimentally trimmed plots than in control plots; however, following Hurricane Maria demographic rates substantially increased in control plots only. In experimentally trimmed plots, the largest community compositional shifts occurred as a result of the trimming events, and compositional changes were greatest for control plots after Hurricane Maria in 2017. Pioneer tree and fern species increased in abundance in response to both simulated and natural hurricanes. Following Hurricane Maria, two dominant pioneer species, Cyathea arborea and Cecropia schreberiana, recruited abundantly, but only in control plots. In trimmed plots, increased solar radiation and soil moisture shifted understory species composition steadily toward pioneer and secondary‐successional species, with soil moisture interacting strongly with canopy trimming. Thus, both solar radiation and soil moisture are environmental drivers affecting pioneer species recruitment following disturbance, which interact with canopy opening following hurricanes. Our results suggest that if hurricane disturbances increase in frequency and severity, as suggested by climate change predictions, the understory regeneration of late‐successional species, such as Manilkara bidentata and Sloanea berteroana, which prefer deeper shade and slightly drier soil microsites, may become imperiled.

Porcine endometrial heat shock proteins are differentially influenced by pregnancy status, heat stress, and altrenogest supplementation during the peri-implantation period.

Heat stress (HS) deleteriously affects multiple components of porcine reproduction and is causal to seasonal infertility. Environment-induced hyperthermia causes a HS response (HSR) typically characterized by increased abundance of intracellular heat shock proteins (HSP). Gilts exposed to HS during the peri-implantation period have compromised embryo survival, however if (or how) HS disrupts the porcine endometrium is not understood. Study objectives were to evaluate the endometrial HSP abundance in response to HS during this period and assess the effect of oral progestin (altrenogest; ALT) supplementation. Postpubertal gilts (n = 42) were artificially inseminated during behavioral estrus (n = 28) or were kept cyclic (n = 14), and randomly assigned to thermal neutral (TN; 21 ± 1 °C) or diurnal HS (35 ± 1 °C for 12 h/31.6 ± 1 °C for 12 h) conditions from day 3 to 12 postestrus (dpe). Seven of the inseminated gilts from each thermal treatment group received ALT (15 mg/d) during this period. Using quantitative PCR, transcript abundance of HSP family A (Hsp70) member 1A (HSPA1A, P = 0.001) and member 6 (HSPA6, P < 0.001), and HSP family B (small) member 8 (HSB8, P = 0.001) were increased while HSP family D (Hsp60) member 1 (HSPD1, P = 0.01) was decreased in the endometrium of pregnant gilts compared to the cyclic gilts. Protein abundance of HSPA1A decreased (P = 0.03) in pregnant gilt endometrium due to HS, while HSP family B (small) member 1 (HSPB1) increased (P = 0.01) due to HS. Oral ALT supplementation during HS reduced the transcript abundance of HSP90α family class B member 1 (HSP90AB1, P = 0.04); but HS increased HSP90AB1 (P = 0.001), HSPA1A (P = 0.02), and HSPA6 (P = 0.04) transcript abundance irrespective of ALT. ALT supplementation decreased HSP90α family class A member 1 (HSP90AA1, P = 0.001) protein abundance, irrespective of thermal environment, whereas ALT only decreased HSPA6 (P = 0.02) protein abundance in TN gilts. These results indicate a notable shift of HSP in the porcine endometrium during the peri-implantation period in response to pregnancy status and heat stress.

Alterations in Skeletal Muscle mRNA Abundance in Response to Ethyl-Cellulose Rumen-Protected Methionine during the Periparturient Period in Dairy Cows.

Simple SummaryImprovements in performance around parturition by feeding ethyl-cellulose rumen-protected methionine (RPM) have been reported. Hepatic and adipose gene transcription effects have been a key focus of studies dealing with RPM. It is unknown, however, if RPM alters the abundance of genes associated with nutrient metabolism and biochemical pathways in skeletal muscle. This tissue also experiences dynamic biological changes around parturition. The objective was to use skeletal muscle biopsies from cows fed a control or RPM-supplemented diet around parturition to investigate alterations in mRNA abundance. Compared with controls, feeding RPM led to overall upregulation of genes associated with amino acid transport, carnitine transport, β-oxidation, vitamin transport, mTOR pathway, insulin signaling, antioxidant response, CDP-Choline pathway, and arginine metabolism. Thus, besides positive effects at the level of performance, RPM can help skeletal muscle maintain homeostasis around parturition partly through alterations in mRNA abundance.This study aimed to evaluate the effect of feeding ethyl cellulose rumen-protected methionine (RPM) on skeletal muscle mRNA abundance during the periparturient period. Sixty multiparous Holstein cows were used in a block design and assigned to either a control or RPM diet. The RPM was supplied from −28 to 60 days in milk (DIM) at a rate of 0.09% (prepartum) or 0.10% (postpartum) of dry matter (DM), ensuring a Lys:Met in the metabolizable protein of ~2.8:1. Muscle biopsies were collected at −21, 1, and 21 DIM. Thirty-five target genes associated with nutrient metabolism and biochemical pathways were measured via RT-qPCR. The mRNA abundance of genes associated with amino acid (AA) transport (SLC7A8, SLC43A2), carnitine transport (SLC22A5), insulin signaling (IRS1), and antioxidant response (NFE2L2) had diet × time effect (p < 0.05) due to greater abundance in RPM versus CON cows, especially at 1 and 21 DIM. Members of the AA transport (SLC7A8, SLC25A29, SCL38A9), fatty acid β-oxidation (ACADVL), vitamin transport (SLC5A6, SLC19A2), mTOR pathway (AKT1 and mTOR), antioxidant response (KEAP1, CUL3), CDP-Choline pathway and arginine metabolism had overall greater abundance (p < 0.05) in RPM versus CON cows. Overall, data indicate that RPM can alter nutrient metabolism in the skeletal muscle around parturition partly through alterations in mRNA abundance.

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways.

MotivationEstimating causal queries, such as changes in protein abundance in response to a perturbation, is a fundamental task in the analysis of biomolecular pathways. The estimation requires experimental measurements on the pathway components. However, in practice many pathway components are left unobserved (latent) because they are either unknown, or difficult to measure. Latent variable models (LVMs) are well-suited for such estimation. Unfortunately, LVM-based estimation of causal queries can be inaccurate when parameters of the latent variables are not uniquely identified, or when the number of latent variables is misspecified. This has limited the use of LVMs for causal inference in biomolecular pathways.ResultsIn this article, we propose a general and practical approach for LVM-based estimation of causal queries. We prove that, despite the challenges above, LVM-based estimators of causal queries are accurate if the queries are identifiable according to Pearl’s do-calculus and describe an algorithm for its estimation. We illustrate the breadth and the practical utility of this approach for estimating causal queries in four synthetic and two experimental case studies, where structures of biomolecular pathways challenge the existing methods for causal query estimation.Availability and implementationThe code and the data documenting all the case studies are available at https://github.com/srtaheri/LVMwithDoCalculus.Supplementary information Supplementary data are available at Bioinformatics online.