Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility

Hematopoietic stem cell lineage choices are decided by genetic networks that are turned ON/OFF in a switch-like manner. However, prior to lineage commitment, genes are primed at low expression levels. Understanding the underlying molecular circuitry in terms of how it governs both a primed state and, at the other extreme, a committed state is of relevance not only to hematopoiesis but also to developmental systems in general. We develop a computational model for the hematopoietic erythroid-myeloid lineage decision, which is determined by a genetic switch involving the genes PU.1 and GATA-1. Dynamical models based upon known interactions between these master genes, such as mutual antagonism and autoregulation, fail to make the system bistable, a desired feature for robust lineage determination. We therefore suggest a new mechanism involving a cofactor that is regulated as well as recruited by one of the master genes to bind to the antagonistic partner that is necessary for bistability and hence switch-like behavior. An interesting fallout from this architecture is that suppression of the cofactor through external means can lead to a loss of cooperativity, and hence to a primed state for PU.1 and GATA-1. The PU.1–GATA-1 switch also interacts with another mutually antagonistic pair, C/EBPα–FOG-1. The latter pair inherits the state of its upstream master genes and further reinforces the decision due to several feedback loops, thereby leading to irreversible commitment. The genetic switch, which handles the erythroid-myeloid lineage decision, is an example of a network that implements both a primed and a committed state by regulating cooperativity through recruitment of cofactors. Perturbing the feedback between the master regulators and downstream targets suggests potential reprogramming strategies. The approach points to a framework for lineage commitment studies in general and could aid the search for lineage-determining genes.     

Metabolomic Analyses of Plasma Reveals New Insights into Asphyxia and Resuscitation in Pigs

Background

Currently, a limited range of biochemical tests for hypoxia are in clinical use. Early diagnostic and functional biomarkers that mirror cellular metabolism and recovery during resuscitation are lacking. We hypothesized that the quantification of metabolites after hypoxia and resuscitation would enable the detection of markers of hypoxia as well as markers enabling the monitoring and evaluation of resuscitation strategies.

Methods and Findings

Hypoxemia of different durations was induced in newborn piglets before randomization for resuscitation with 21% or 100% oxygen for 15 min or prolonged hyperoxia. Metabolites were measured in plasma taken before and after hypoxia as well as after resuscitation. Lactate, pH and base deficit did not correlate with the duration of hypoxia. In contrast to these, we detected the ratios of alanine to branched chained amino acids (Ala/BCAA; R².adj = 0.58, q-value<0.001) and of glycine to BCAA (Gly/BCAA; R².adj = 0.45, q-value<0.005), which were highly correlated with the duration of hypoxia. Combinations of metabolites and ratios increased the correlation to R²adjust = 0.92. Reoxygenation with 100% oxygen delayed cellular metabolic recovery. Reoxygenation with different concentrations of oxygen reduced lactate levels to a similar extent. In contrast, metabolites of the Krebs cycle (which is directly linked to mitochondrial function) including alpha keto-glutarate, succinate and fumarate were significantly reduced at different rates depending on the resuscitation, showing a delay in recovery in the 100% reoxygenation groups. Additional metabolites showing different responses to reoxygenation include oxysterols and acylcarnitines (n = 8–11, q<0.001).

Conclusions

This study provides a novel strategy and set of biomarkers. It provides biochemical in vivo data that resuscitation with 100% oxygen delays cellular recovery. In addition, the oxysterol increase raises concerns about the safety of 100% O₂ resuscitation. Our biomarkers can be used in a broad clinical setting for evaluation or the prediction of damage in conditions associated with low tissue oxygenation in both infancy and adulthood. These findings have to be validated in human trials.     

Anaemia,Zinc and Copper Deficiencies Among Pregnant Women in Central Sudan

Anaemia is a widespread problem in many parts of the world especially in tropic areas. Among pregnant women, it has negative consequences on maternal and perinatal outcomes. A cross-sectional study was conducted to investigate the prevalence of anaemia, iron, zinc and copper deficiencies among pregnant women in Wad Medani hospital, central Sudan and to examine the relationship of these micronutrients with haemoglobin (Hb) levels. One hundred four (52.5%) out of 200 pregnant women had anaemia (Hb < 11 gm/dl) and 3 (1.5) % had severe anaemia (Hb < 7 gm/dl). Iron deficiency (S-ferritin < 15 μg/l), iron deficiency anaemia (<11 gm/dl and S-ferritin < 15 μg/l) were prevalent in 25 (12.5%) and 13 (6.5%) of these women, respectively. Ninety (45.0%) and eight (4.0%) of these women had zinc (<80 μg/ml) and copper (<80 μg/ml) deficiency, respectively. In 24 (12.0%) of these women, there were ≥2 deficiencies of these elements. S-copper was significantly lower in patients with anaemia. While age, parity, gestational age, ferritin, zinc and copper were not predictors for anaemia, women who practiced pica were at higher risk for anaemia (OR = 3.4, 95% CI = 1.4–7.9, P = 0.004). Gestational age was significantly inversely correlated with haemoglobin (r = 0.161, P = 0.03), S-ferritin (r = 0.285, P = 0.001) and S-zinc (r = 0.166, P = 0.02). Thus, dietary and supplement interventions are required to prevent and control anaemia in this setting. Further research is needed.     

Prehistoric settlement activities changed soil pH, nutrient availability, and growth of contemporary crops in Central Europe

Background and aims

How prehistoric human settlement activities have changed soil chemical properties, plant nutrition and growth of contemporary crops is a question that has not been satisfactorily addressed. The aim of this paper was to study to what extent nutrient availability in the soil, together with nutrition and growth of spring barley (Hordeum vulgare), improved on sites of former sunken buildings (cropmarks) in comparison to their surroundings (controls) 1,700 years after abandonment of the buildings.

Methods

In the Czech Republic, a unique prehistoric settlement with many sunken buildings was discovered during aerial reconnaissance from cropmarks in stands of cereals. Soil and biomass samples were collected from cropmarks and controls in a barley crop in June 2012.

Results

A substantially higher content of organic matter, higher pH and concentrations of plant-available (Mehlich III) P, Ca, Mg, Cu and Zn were recorded in the sub-soil layer in cropmarks compared with controls, indicating the accumulation of wood ash and organic waste. In the arable layer, pH and concentrations of P, Ca and Mg were generally very high in both positions. Cropmarks were characterised by barley plants that were twice as tall as the controls, with significantly higher Ca, Mg and P concentrations.

Conclusions

Prehistoric settlement activity affected nutrient availability and plant growth in the previously settled area even after 1,700 years. We conclude that the chemical signature of prehistoric settlement activity can be detected from chemical analysis of the sub-soil layer as well as analysis of the contemporary arable layer and crop biomass.     

Food Choices and Consequences for the Nutritional Status: Insights into Nutrition Transition in an Hospital Community

Introduction

Although economic development is generally accompanied by improvements in the overall nutritional status of the country’s population the ‘nutritional transition’ often involves a shift to high energy diets and less exercise with negative consequences. This pilot study was done to examine if education of parents operates at the household level to influence dietary choices and the nutritional status of children in a small community of hospital workers.

Material and Methods

3 groups of persons with varying skill and education levels participated. Weighed food logs were used in all households to calculate ‘adult equivalent’ per-capita-consumption. Nutrients were calculated using nutrients calculator software. BMI was used to classify children as underweight, normal weight and overweight.

Results

128 individuals participated from 30 families included 47 children. 10 children (21%) were underweight, 29 (62%) were normal and 8 (17%) were overweight. Energy consumption was highest in families with overweight children 2692 +/-502 compared to 2259 +/-359 in families with normal weight and 2031+/-354 in the family of underweight children. These differences were statistically significant. 42% underweight children belonged to Class 1 at the lowest skill level and there were no overweight children in this group. Most of the overweight children belonged to Class 2. In Class 3 there were no underweight children and the majority was normal weight children.

Conclusion

Underweight children came from the poorer households. Per capita intake of the family as a whole correlated well with BMI in the children. There was increased obesity in middle income families belonging to Class 2—probably in families who move up the scale from deprivation. Nutritional status in children correlated mostly with maternal education status.     

Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates

The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92%) of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S. cerevisiae.     

Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State

The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum (ER)-derived vesicles to create an organelle designated Legionella-containing vacuole (LCV) required for bacterial replication. Maturation of the LCV involved acquisition of Rab1, which is mediated by the bacterial effector protein SidM/DrrA. SidM/DrrA is a bifunctional enzyme having the activity of both Rab1-specific GDP dissociation inhibitor (GDI) displacement factor (GDF) and guanine nucleotide exchange factor (GEF). LidA, another Rab1-interacting bacterial effector protein, was reported to promote SidM/DrrA-mediated recruitment of Rab1 to the LCV as well. Here we report the crystal structures of LidA complexes with GDP- and GTP-bound Rab1 respectively. Structural comparison revealed that GDP-Rab1 bound by LidA exhibits an active and nearly identical conformation with that of GTP-Rab1, suggesting that LidA can disrupt the switch function of Rab1 and render it persistently active. As with GTP, LidA maintains GDP-Rab1 in the active conformation through interaction with its two conserved switch regions. Consistent with the structural observations, biochemical assays showed that LidA binds to GDP- and GTP-Rab1 equally well with an affinity approximately 7.5 nM. We propose that the tight interaction with Rab1 allows LidA to facilitate SidM/DrrA-catalyzed release of Rab1 from GDIs. Taken together, our results support a unique mechanism by which a bacterial effector protein regulates Rab1 recycling.     

Mass Spectrometry Reveals New Insights into the Production of Superoxide Anions and 4‐Hydroxynonenal Adducted Proteins in Human Sperm

The free‐radical theory of male infertility suggests that reactive oxygen species produced by the spermatozoa themselves are a leading cause of sperm dysfunction, including loss of sperm motility. However, the field is overshadowed on several fronts, primarily because: i) the probes used to measure reactive oxygen species (ROS) are imprecise; and ii) many reports suggesting that oxygen radicals are detrimental to sperm function add an exogenous source of ROS. Herein, a more reliable approach to measure superoxide anion production by human spermatozoa based on MS analysis is used. Furthermore, the formation of the lipid‐peroxidation product 4‐hydroxynonenal (4‐HNE) during in vitro incubation using proteomics is also investigated. The data demonstrate that neither superoxide anion nor other free radicals that cause 4‐HNE production are related to the loss of sperm motility during incubation. Interestingly, it appears that many of the 4‐HNE adducted proteins, found within spermatozoa, originate from the prostate. A quantitative SWATH analysis demonstrate that these proteins transiently bind to sperm and are then shed during in vitro incubation. These proteomics‐based findings propose a revised understanding of oxidative stress within the male reproductive tract.     

Food and feeding habits of Labeo niloticus (Pisces,Cyprinidae) in Jebel Aulia Reservoir,Sudan

Basic knowledge on the feeding ecology of one of the common and commercially important fish species in Jebel Aulia Reservoir is provided.The structure of the feeding apparatus indicates that Labeo niloticus is a bottom feeder, depending on soft and decayed vegetation, organic debris and whatever small organisms found within. However, juveniles and fry are prone to explore all layers and depths of the river selectively for plankton. There is little evidence of seasonal selection of food. Changes in diet quality are governed by the availability of type of food. Variability of feeding activity is connected with climate and breeding season.     

Animal-Borne Imaging Reveals Novel Insights into the Foraging Behaviors and Diel Activity of a Large-Bodied Apex Predator,the American Alligator (Alligator mississippiensis)

Large-bodied, top- and apex predators (e.g., crocodilians, sharks, wolves, killer whales) can exert strong top-down effects within ecological communities through their interactions with prey. Due to inherent difficulties while studying the behavior of these often dangerous predatory species, relatively little is known regarding their feeding behaviors and activity patterns, information that is essential to understanding their role in regulating food web dynamics and ecological processes. Here we use animal-borne imaging systems (Crittercam) to study the foraging behavior and activity patterns of a cryptic, large-bodied predator, the American alligator (Alligator mississippiensis) in two estuaries of coastal Florida, USA. Using retrieved video data we examine the variation in foraging behaviors and activity patterns due to abiotic factors. We found the frequency of prey-attacks (mean = 0.49 prey attacks/hour) as well as the probability of prey-capture success (mean = 0.52 per attack) were significantly affected by time of day. Alligators attempted to capture prey most frequently during the night. Probability of prey-capture success per attack was highest during morning hours and sequentially lower during day, night, and sunset, respectively. Position in the water column also significantly affected prey-capture success, as individuals’ experienced two-fold greater success when attacking prey while submerged. These estimates are the first for wild adult American alligators and one of the few examples for any crocodilian species worldwide. More broadly, these results reveal that our understandings of crocodilian foraging behaviors are biased due to previous studies containing limited observations of cryptic and nocturnal foraging interactions. Our results can be used to inform greater understanding regarding the top-down effects of American alligators in estuarine food webs. Additionally, our results highlight the importance and power of using animal-borne imaging when studying the behavior of elusive large-bodied, apex predators, as it provides critical insights into their trophic and behavioral interactions.     

Food and feeding relationships of fish in the Sudd swamps (River Nile, southern Sudan)

The gut contents of 37 species of R. Nile fish are described. Classification according to diet shows four species to be mud-feeders, three to be microherbivores, two to be macroherbivores and five to be omnivores. The remaining majority (23) are categorized as carnivorous and comprise one neuston-feeder, one zooplanktivore, six bottom-feeders, seven browsers in vegetation and eight macropredators. Food webs are proposed for three major ecological zones, namely the open-water and submerged vegetation of a river-lake, the floating fringe of Eichhornia crassipes and the seasonally flooded grassland.     

Quantitative Analysis of the Chloroplast Molecular Chaperone ClpC/Hsp93 in Arabidopsis Reveals New Insights into Its Localization,Interaction with the Clp Proteolytic Core,and Functional Importance

The molecular chaperone ClpC/Hsp93 is essential for chloroplast function in vascular plants. ClpC has long been held to act both independently and as the regulatory partner for the ATP-dependent Clp protease, and yet this and many other important characteristics remain unclear. In this study, we reveal that of the two near-identical ClpC paralogs (ClpC1 and ClpC2) in Arabidopsis chloroplasts, along with the closely related ClpD, it is ClpC1 that is the most abundant throughout leaf maturation. An unexpectedly large proportion of both chloroplast ClpC proteins (30% of total ClpC content) associates to envelope membranes in addition to their stromal localization. The Clp proteolytic core is also bound to envelope membranes, the amount of which is sufficient to bind to all the similarly localized ClpC. The role of such an envelope membrane Clp protease remains unclear although it appears uninvolved in preprotein processing or Tic subunit protein turnover. Within the stroma, the amount of oligomeric ClpC protein is less than that of the Clp proteolytic core, suggesting most if not all stromal ClpC functions as part of the Clp protease; a proposal supported by the near abolition of Clp degradation activity in the clpC1 knock-out mutant. Overall, ClpC appears to function primarily within the Clp protease, as the principle stromal protease responsible for maintaining homeostasis, and also on the envelope membrane where it possibly confers a novel protein quality control mechanism for chloroplast preprotein import.     

Plant sexual systems, dichogamy, and herkogamy in the Venezuelan Central Plain

Sexual system, temporal variation in sex expression, and herkogamy were evaluated in 210 plant species in the Venezuelan Central Plain (VCP). This analysis was conducted considering the life forms, habitats, flowering time, pollination systems, and dispersal syndromes of the plant species. Hermaphrodite species dominated the community (75.2%; N=158), followed by monoecious taxa (17.1%; N=36), and then dioecious (7.6; N=16). Most species were adichogamous (=homogamous) (75.2%; N=155), followed by protandrous (16.5%; N=34), and protogynous (8.3%; N=17). The frequency of herkogamous species was higher (N=124; 60.2%) than the non-herkogamous (N=82; 39.8%). The three reproductive traits interacted significantly in a way that complements their effectiveness in promoting cross-pollination and avoidance of pollen–stigma interference: hermaphrodite-adichogamous species occurred in similar frequency to herkogamous and non-herkogamous species; monoecious-adichogamous species were mostly herkogamous, and all hermaphrodite, functionally dioecious-adichogamous, species were herkogamous. Sexual system, herkogamy, and dichogamy are associated with habitats in the savanna-forest mosaic of the VCP. The proportion of dioecious species decreased from trees to annual herbs and from forest to disturbed areas. Dichogamous species were most frequent for herbaceous plants, and non-herkogamous species dominated in annual herbs. The frequency of herkogamous species decreased from forest to disturbed areas. Sexual system was significantly associated with pollination system. Most dioecious and monoecious species had generalist pollination. A three-factor log linear analysis indicated that for any combination significantly. Sexual systems and herkogamy were associated with the respective seed dispersal syndrome. Most dioecious and herkogamous species were dispersed by frugivores, while monoecious plants tended to be dispersed by granivores and wind. Flowering time of dioecious species peaked during the dry–rainy transition period, whereas that of monoecious species was greatest during the rainy season. Therefore, specific biotic and abiotic conditions may enforce the occurrence of unisexuality in the community. In a similar way, dichogamous species tend to flower during the rainy season, associated with herbaceous life form and wind pollination. These results are discussed in the context of evolutionary and ecological trends.