Search

Prey refuge from predators can play an important role in stabilising an ecological system by reducing interactions between species, while Allee effects can arise from a range of biological phenomena, such as anti-predator vigilance, genetic trends and feeding deficiencies. We develop a predator–prey model that combines these phenomena, considering variable prey refuge with additive Allee effect on the prey species, with a Holling type II response function for the prey growth function. We use the predator and prey nullclines to determine the existence and stability of interior equilibria. We also investigate all possible local and global bifurcations that the system could undergo, showing that prey refuge and a strong Allee effect can lead to saddle-node bifurcations, Hopf bifurcations or Bogdanov–Takens bifurcation. We have investigated the appearance of Hopf bifurcations in a neighborhood of the unique interior equilibrium point of the dynamical system. The rich behaviour of the dynamics suggests that both prey refuge and a strong Allee affect are important factors in ecological complexity.

Initial work to generate physically robust biofilms for biocatalytic applications revealed that Escherichia coli K-12 can form a floating biofilm at the air-liquid interface, commonly referred to as a pellicle. Unlike other species where pellicle formation is well-characterised, such as Bacillus subtilis, there are few reports of E. coli K-12 pellicles in the literature. In order to study pellicle formation, a growth model was developed and pellicle formation was monitored over time. Mechanical forces, both motility and shaking, were shown to have effects on pellicle formation and development. The role and regulation of curli, an amyloid protein adhesin critical in E. coli K-12 biofilm formation, was studied by using promoter-green fluorescent protein reporters; flow cytometry and confocal laser scanning microscopy were used to monitor curli expression over time and in different locations. Curli were found to be not only crucial for pellicle formation, but also heterogeneously expressed within the pellicle. The components of the extracellular polymeric substances (EPS) in pellicles were analysed by confocal microscopy using lectins, revealing distinct pellicle morphology on the air-facing and medium-facing sides, and spatially- and temporally-regulated generation of the EPS components poly-N-acetyl glucosamine and colanic acid. We discuss the difference between pellicles formed by E. coli K-12, pathogenic E. coli strains and other species, and the relationship between E. coli K-12 pellicles and solid surface-attached biofilms.

Crapemyrtle bark scale (CMBS; Acanthococcus lagerstroemiae Kuwana) is an invasive insect that was first discovered in the United States in 2004. The polyphagous feeding habit of CMBS has allowed it to infest a wide range of plant species beyond its primary host, Lagerstroemia. Using molecular approaches, we studied the genetic relationships between CMBS specimens and their hosts from different geographic locations. Naturally occurring CMBS infestations were confirmed on American beautyberry (Callicarpa americana L.), a native plant species in the United States, and spirea (Spiraea L.). The new infestation of CMBS found on Spiraea raises the alarm that other economically important crops in the Amygdaloideae subfamily (subfamily under Rosaceae) might be susceptible to CMBS attacks.

Objectives: Although fermented food use is ubiquitous in humans, the ecological and evolutionary factors contributing to its emergence are unclear. Here we investigated the ecological contexts surrounding the consumption of fruits in the late stages of fermentation by wild primates to provide insight into its adaptive function. We hypothesized that climate, socioecological traits, and habitat patch size would influence the occurrence of this behavior due to effects on the environmental prevalence of late-stage fermented foods, the ability of primates to detect them, and potential nutritional benefits. Materials and methods: We compiled data from field studies lasting at least 9 months to describe the contexts in which primates were observed consuming fruits in the late stages of fermentation. Using generalized linear mixed-effects models, we assessed the effects of 18 predictor variables on the occurrence of fermented food use in primates. Results: Late-stage fermented foods were consumed by a wide taxonomic breadth of primates. However, they generally made up 0.01%–3% of the annual diet and were limited to a subset of fruit species, many of which are reported to have mechanical and chemical defenses against herbivores when not fermented. Additionally, latestage fermented food consumption was best predicted by climate and habitat patch size. It was more likely to occur in larger habitat patches with lower annual mean rainfall and higher annual mean maximum temperatures. Discussion: We posit that primates capitalize on the natural fermentation of some fruits as part of a nutritional strategy to maximize periods of fruit exploitation and/or access a wider range of plant species. We speculate that these factors contributed to the evolutionary emergence of the human propensity for fermented foods. Canadian Institute for Advanced Research/[]/CIFAR/Canadá UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biología

Interleukin‐31 (IL‐31) is a Th2 cell–derived cytokine that has been closely linked to pruritic skin inflammation. More recently, enhanced IL‐31 serum levels have also been observed in patients with allergic rhinitis and allergic asthma. Therefore, the main aim of this study was to unravel the contribution of IL‐31 to allergen‐induced lung inflammation. We analyzed lung inflammation in response to the timothy grass (Phleum pratense) pollen allergen Phl p 5 in C57BL/6 wild‐type (wt) mice, IL‐31 transgenic (IL‐31tg) mice, and IL‐31 receptor alpha‐deficient animals (IL‐31RA−/−). IL‐31 and IL‐31RA levels were monitored by qRT‐PCR. Cellular infiltrate in bronchoalveolar lavage fluid (BALF) and lung tissue inflammation, mucus production as well as epithelial thickness were measured by flow cytometry and histomorphology. While allergen challenge induced IL‐31RA expression in lung tissue of wt and IL‐31tg mice, high IL‐31 expression was exclusively observed in lung tissue of IL‐31tg mice. Upon Phl p 5 challenge, IL‐31tg mice showed reduced numbers of leukocytes and eosinophils in BALF and lung tissue as well as diminished mucin expression and less pronounced epithelial thickening compared to IL‐31RA−/− or wt animals. These findings suggest that the IL‐31/IL‐31RA axis may regulate local, allergen‐induced inflammation in the lungs., This study describes a role for IL‐31 signaling in the context of allergen‐induced lung inflammation. Mice overexpressing IL‐31 develop less severe lung inflammation upon allergen exposure, characterized by decreased leukocyte infiltration, mucus production and epithelial thickening. Thus, our data indicate that IL‐31 signaling regulates allergen‐induced lung inflammation.

Two Gram-stain-negative, strictly aerobic, marine bacteria, designated as strains RKSG066T and RKSG123T, were isolated from a sponge Aplysina fistularis collected at a depth of 15 m off the west coast of San Salvador, The Bahamas. Investigation of nearly full-length 16S rRNA gene and whole genome-based phylogenies revealed that both strains belong to the order Cytophagales within the class Cytophagia and phylum Bacteroidetes . Strain RKSG066T formed a monophyletic clade with described members of the genus Fulvivirga , while strain RKSG123T formed a well-supported paraphyletic branch apart from this and other related genera within the family Flammeovirgaceae . For both RKSG066T and RKSG123T, optimal growth parameters were 30–37 °C, pH 7–8 and 2–3 % (w/v) NaCl; cells were catalase- and oxidase-positive, and flexirubin-type pigments were absent. The predominant fatty acids were iso-C15 : 0, C16 : 0, C18 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0 3-OH, C18 : 1 ω9c and iso-C15 : 1 G for RKSG066T, and iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0, C16 : 0 3-OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) for RKSG123T. Menaquinone-7 was the major respiratory quinone for both strains. The DNA G+C contents of RKSG066T and RKSG123T were 39.5 and 36.7 mol%, respectively. On the basis of phylogenetic distinctiveness and polyphasic analysis, the type strain RKSG066T (=TSD-73T=LMG 29870T) is proposed to represent a novel species of the genus Fulvivirga , for which the name Fulvivirga aurantia sp. nov. is proposed. The type strain RKSG123T (=TSD-75T=LMG 30075T) is proposed to represent the type species of a novel genus and species with the proposed name Xanthovirga aplysinae gen. nov., sp. nov. Additionally, the genus Fulvivirga is emended to include strains of orange-pigmented colonies that contain the predominant cellular fatty acids C16 : 0, C18 : 0, C16 : 1 ω5c and C18 : 1 ω9c.

A Gram-stain-negative, strictly aerobic, motile bacterium, designated strain RKSG073T, was isolated from the sea sponge Aplysina fistularis, collected off the west coast of San Salvador, The Bahamas. Cells were curved-to-spiral rods with single, bipolar (amphitrichous) flagella, oxidase- and catalase-positive, non-nitrate-reducing and required salt for growth. RKSG073T grew optimally at 30–37 °C, pH 6–7, and with 2–3 % (w/v) NaCl. The predominant fatty acids of RKSG073T were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. Major isoprenoid quinones were identified as Q-10 and Q-9. Phylogenetic analyses of nearly complete 16S rRNA genes and genome sequences positioned strain RKSG073T in a clade with its closest relative Aestuariispira insulae AH-MY2T (92.1 % 16S rRNA gene sequence similarity), which subsequently clustered with Hwanghaeella grinnelliae Gri0909T, Marivibrio halodurans ZC80T and type species of the genera Kiloniella , Thalassospira and Terasakiella . The DNA G+C content calculated from the genome of RKSG073T was 42.2 mol%. On the basis of phylogenetic distinctiveness and polyphasic analysis, here we propose that RKSG073T (culture deposit numbers: ATCC collection = TSD-74T, BCCM collection = LMG 29869T) represents the type strain of a novel genus and species within the family Kiloniellaceae , order Rhodospirillales and class Alphaproteobacteria , for which the name Curvivirga aplysinae gen. nov., sp. nov. is proposed.

Biofilm formation is a harmful phenomenon in many areas, such as in industry and clinically, but offers advantages in the field of biocatalysis for the generation of robust biocatalytic platforms. In this work, we optimised growth conditions for the production of Escherichia coli biofilms by three strains (PHL644, a K-12 derivative with enhanced expression of the adhesin curli; the commercially-used strain BL21; and the probiotic Nissle 1917) on a variety of surfaces (plastics, stainless steel and PTFE). E. coli PHL644 and PTFE were chosen as optimal strain and substratum, respectively, and conditions (including medium, temperature, and glucose concentration) for biofilm growth were determined. Finally, the impact of these growth conditions on expression of the curli genes was determined using flow cytometry for planktonic and sedimented cells. We reveal new insights into the formation of biofilms and expression of curli in E. coli K-12 in response to environmental conditions. Electronic supplementary material The online version of this article (10.1007/s00203-020-01864-5) contains supplementary material, which is available to authorized users.

An improved understanding of interaction dynamics between dolphins and trawlers is essential for improving bycatch mitigation strategies. In-situ observations using video at increasing distances from the net opening during 50 commercial fish trawls, recorded 5908 common bottlenose dolphin (Tursiops truncatus (Montagu, 1821)) interactions and provided details on their duration, depredation rates, and behaviours. Dolphin interactions with trawls were very common (98% of day-trawls, 118 ± 16 interactions per trawl), with durations and prey consumption positively correlated with the distances ventured into the net. Acoustic deterrents (pingers) had no effect on interaction numbers or durations. Based on in-situ observations, the factors that contribute toward dolphin bycatch in demersal fish trawls were likely associated with (i) risky dolphin behaviour (i.e., entering net during hauling, residing deep within trawl for extended periods or social aggression) and (or) (ii) instability of fishing gear resulting in entrapment. Given the high level of dolphin attendance during most day-trawls, mitigation strategies that focus on improving and monitoring the stability of trawl gear would be more effective than current acoustic deterrent devices aimed at modifying dolphin behaviour.

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain RKSG058T, was isolated from the marine sponge Verongula gigantea, collected off the west coast of San Salvador, The Bahamas. Phylogenetic analyses based on 16S rRNA gene sequences revealed that RKSG058T formed a distinct lineage within the family Hahellaceae (order Oceanospirillales , class Gammaproteobacteria ), and was most closely related to the genus Endozoicomonas , with sequence similarities to members of this genus ranging from 92.0 to 93.7 %. Optimal growth occurred at 30 °C, at pH 7 and in the presence of 2–3 % (w/v) NaCl. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The major and minor respiratory quinones were Q-9 and Q-8, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid and five unidentified lipids. The DNA G+C content was 42.3 mol%. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strain RKSG058T represents the first cultured isolate of a novel bacterial genus and species within the family Hahellaceae , for which the name Sansalvadorimonas verongulae gen. nov., sp. nov. is proposed. The type strain of Sansalvadorimonas verongulae is RKSG058T (=TSD-72T=LMG 29871T). An emended description of the genus Kistimonas is provided.

Dietary data are used to categorize species diets, but these categorizations do not take into account the mutability of food resources in time or space, the level of interspecific competition in various communities as these resources change, nor the dietary flexibility of species. In this study, we assess the diets of three sympatric species, Eulemur rufifrons, Propithecus edwardsi, and Varecia variegata, in the Vatoharanana site in Ranomafana National Park, Madagascar. We determine dietary diversity, overlap, and interannual variation with data collected from 2001 to 2003. We then compare results on food preference and time feeding with data collected on each species in the late 1980s and early 1990s to determine whether these findings are consistent over the long term. We found little interannual variation in the proportion of time spent eating particular plant parts for each of the lemur species during the three study years (2001–2003), and between the earlier and current study. Food items were not always consumed based solely on availability. Dietary diversity was lower in the two frugivorous species (V. variegata and E. rufifrons) compared with the folivorous species (P. edwardsi), and V. variegata and E. rufifrons were more likely to focus their feeding time on one particular genus and plant part in each year. The study species used different strategies to deal with food, particularly fruit, shortages such as a plastic social structure (V. variegata), habitat shifting (E. rufifrons), and dietary switching (P. edwardsi). Although there was low dietary overlap between the study species, they depended on a small number of shared fruits in each of the study years (Chrysophyllum, Syzygium, Ocotea, Plagioscyphus), which may indicate some potential for interspecific competition. Because these lemur species, like all primates, lead relatively long lives (avg. >30 years) and have slow rates of aging, longitudinal studies are needed to test hypotheses reliant on basic dietary information.

Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based on circumstantial evidence. We provide the first direct measurement of the effects of transformation on a fungal genome by sequencing the genomes of 29 transformants and 30 untransformed controls with high coverage. Contrary to the received wisdom, our results show that transformation of DNA segments flanked by long targeting sequences, followed by homologous recombination and selection for a drug marker, is extremely safe. If a transformation deletes a gene, that may create selective pressure for a few compensatory mutations, but even when we deleted a gene, we found fewer than two point mutations per deletion strain, on average. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between the wild type and strains modified by genomic insertion of a drug resistance marker. As part of our report, we provide the assembled genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99α.

Myeloid-derived suppressor cells (MDSCs) are immature myeloid cells critical in mediating immune suppression in cancer patients. To develop an in vitro assay system that functionally mimics the tumor microenvironment, we cultured human monocytes with conditioned media from several cancer cell lines. Conditioned media from five tumor cell lines induced survival and differentiation of monocytes into cells characteristically similar to macrophages and MDSCs. Notably, media from the 786.O renal cell carcinoma line induced monocytes to acquire a monocytic MDSC phenotype characterized by decreased HLA-DR expression, increased nitric oxide production, enhanced proliferation, and ability to suppress autologous CD3+ T cell proliferation. We further demonstrated that these in vitro MDSCs are phenotypically and functionally similar to patient-derived MDSCs. Inhibitors of STAT3, CK2, and GM-CSF resulted in partial reversal of the MDSC phenotype. MDSCs generated in vitro from 786.O tumor conditioned media represent a platform to identify potential therapeutics that inhibit MDSC activities.

Vertebrate gut microbiota form a key component of immunity and a dynamic link between an individual and the ecosystem. Microbiota might play a role in social systems as well, because microbes are transmitted during social contact and can affect host behaviour. Combining methods from behavioural and molecular research, we describe the relationship between social dynamics and gut microbiota of a group-living cooperative species of primate, the red-bellied lemur (Eulemur rubriventer). Specifically, we ask whether patterns of social contact (group membership, group size, position in social network, individual sociality) are associated with patterns of gut microbial composition (diversity and similarity) between individuals and across time. Red-bellied lemurs were found to have gut microbiota with slight temporal fluctuations and strong social group-specific composition. Contrary to expectations, individual sociality was negatively associated with gut microbial diversity. However, position within the social network predicted gut microbial composition. These results emphasize the role of the social environment in determining the microbiota of adult animals. Since social transmission of gut microbiota has the potential to enhance immunity, microbiota might have played an escalating role in the evolution of sociality.

Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome. Fil: Mann, Allison E.. University of British Columbia; Canadá Fil: Mazel, Florent. University of British Columbia; Canadá Fil: Lemay, Matthew A.. University of British Columbia; Canadá Fil: Morien, Evan. University of British Columbia; Canadá Fil: Billy, Vincent. University of British Columbia; Canadá Fil: Kowalewski, Miguel Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia". Estación Biológica de Usos Múltiples (Sede Corrientes); Argentina Fil: Di Fiore, Anthony. University of Texas at Austin; Estados Unidos Fil: Link, Andrés. Universidad de los Andes; Colombia Fil: Goldberg, Tony L.. University of Wisconsin; Estados Unidos Fil: Tecot, Stacey. University of Arizona; Estados Unidos Fil: Baden, Andrea L.. City University Of New York. Hunter College; Estados Unidos Fil: Gomez, Andres. University of Minnesota; Estados Unidos Fil: Sauther, Michelle L.. State University of Colorado at Boulder; Estados Unidos Fil: Cuozzo, Frank P.. Lajuma Research Centre; Sudáfrica Fil: Rice, Gillian A. O.. Dartmouth College; Estados Unidos Fil: Dominy, Nathaniel J.. Dartmouth College; Estados Unidos Fil: Stumpf, Rebecca. University of Illinois at Urbana; Estados Unidos Fil: Lewis, Rebecca J.. University of Texas at Austin; Estados Unidos Fil: Swedell, Larissa. University of Cape Town; Sudáfrica. City University of New York; Estados Unidos Fil: Amato, Katherine. Northwestern University; Estados Unidos Fil: Wegener Parfrey, Laura. University of British Columbia; Canadá

A Rock Alpine doe ( Capra aegagrus hircus) was presented to the Colorado State University Veterinary Teaching Hospital because of scaling and ulceration over the withers, coronary bands, and dewclaws. The doe was euthanized because of poor prognosis associated with a radiographically identified cranial mediastinal mass, increased respiratory effort, and discomfort. Autopsy revealed a cranial mediastinal mass, and scaling-to-ulcerative lesions affecting the dorsum, ventrum, pinna, neck, teats, coronary bands, and dewclaws. Histologically, the mediastinal mass was an epithelial neoplasm with admixed non-neoplastic T lymphocytes, consistent with a lymphoepithelial (mixed) thymoma. Sections of affected skin were characterized by hyperkeratotic cell-rich interface dermatitis with transepidermal and follicular apoptosis. Thymoma-associated exfoliative dermatitis has been recognized in cats and a rabbit, but has not been reported previously in a goat, to our knowledge. Given that thymomas are not uncommon in goats, thymoma-associated exfoliative dermatitis should be considered a clinical differential in goats with dermatologic disease.

We provide a preliminary case study in red-bellied lemurs (Eulemur rubriventer) to illustrate a multimodal approach to understanding communication strategies within a species with obligate pair-bonds. From June to August 2012, we observed and analyzed signaling behaviors across three established red-bellied lemur pairs at Duke Lemur Center (Durham, NC, USA). Our aim was to assess how individuals combine signal modalities to communicate with pair-mates, and to determine whether these strategies vary by time of day, sex, or pair. We analyzed rates of occurrence of touch (allogrooming, mutual grooming, physical contact, and huddling), scent (scent marking and allomarking), and sound (close-distance contact calls) using Wilcoxon rank sum and exact binomial tests. Time of day impacted rates of occurrence across signal modalities, with higher rates of combined signaling within each modality occurring earlier in the day (p 0.03). Across time periods, all pairs used auditory signals most frequently, followed by olfactory signals, and finally tactile and tactile-olfactory signals (p 0.01, all comparisons). In fact, auditory signals frequently overlapped the olfactory signaling modality, and travel rarely occurred without accompanying vocalizations. However, red-bellied lemurs spent the highest percentage of their observed time in tactile signaling bouts (on average, 19.5% of total observed time across pairs). Males and females participated equally in most signaling behaviors (p 0.1), with the exception of scent marking, which males used more frequently (p 0.01). The results of this study will aid in developing methods and hypotheses to determine how wild red-bellied lemurs communicate to form, maintain, and advertise their pair-bonds.

We measured faecal glucocorticoid metabolites (GCs) in Critically Endangered diademed sifaka to understand how food availability, nutritional intake and habitat disturbance impact stress physiology. GCs elevated with food scarcity and correlated negatively with feeding time. Attenuated GCs in fragmented forest groups suggest a downregulated response to a chronically poor environment., Glucocorticoids are metabolic byproducts of animals’ physiological responses to ecological or social challenges and are thought to represent an adaptive response allowing beneficial responses to short-term challenges. Glucocorticoid metabolites (GCs) can be assayed non-invasively through faeces and therefore can be a useful tool to gauge the health of populations experiencing natural and/or anthropogenic stressors. However, the response of GCs to anthropogenic stressors varies, with both higher and lower GC levels reported. Here, we describe variation in GC secretion within eight diademed sifaka (Propithecus diadema) groups across 1 year. These groups span a gradient of anthropogenic habitat disturbance, including groups in continuous forest (‘CONT’) and disturbed fragments (‘FRAG’), and indicators of health suggest that FRAG groups are negatively impacted by habitat disturbance. We monitored phenology, used focal animal follows to quantify diet and collected faeces (n = 547) from which we quantified GC content using enzyme immunoassay. All groups showed elevated lean-season GCs, but with a single, brief peak. GCs were inversely correlated with feeding time. No overall effect of habitat (CONT vs. FRAG) was found, but the lean-season peak was significantly higher in CONT groups. There was a significant season*age–sex interaction; adult females had an attenuated lean-season response compared with groupmates. The observed lean-season ‘challenge’ is consistent with previous lemur studies, as well as mammals in general. Low and largely invariable GC levels in FRAG, within the context of observed health and nutritional declines, suggest that FRAG groups employ a strategy whereby the adrenal response to stressors is downregulated. More research is needed to contextualize our observations of GC variation and health on an individual level, both in terms of corroborating evidence for ecological and social stressors, and longer-term quantification of reproductive success and fitness.

Background:BAFF and APRIL are TNF superfamily members that form homo- and heteromultimers that bind TACI and BCMA on B cells; BAFF also binds BAFF-R. BAFF and APRIL support B cell development, differentiation, and survival, particularly for plasmablasts and plasma cells, and play critical roles in the pathogenesis of B cell-related autoimmune diseases. In nonclinical models, inhibition of either BAFF or APRIL alone mediates relatively modest effects, whereas their co-neutralization dramatically reduces B cell function, including antibody production. Fc fusions of wild-type (WT) TACI (e.g. atacicept and telitacicept) target both BAFF and APRIL and have demonstrated promising clinical potential in e.g. systemic lupus erythematosus (SLE) and IgA nephropathy but have not yet clearly exhibited long-term and/or complete disease remissions.Objectives:To generate a dual BAFF/APRIL antagonist with inhibitory activity superior to WT TACI and BCMA and with the potential to improve clinical outcomes in B cell-mediated diseases.Methods:Our directed evolution platform was used to identify a potent variant TNFR domain (vTD) of TACI that exhibits significantly enhanced affinity for BAFF and APRIL as compared to WT TACI; this TACI vTD domain was fused to a human IgG Fc to generate the therapeutic candidate ALPN-303. ALPN-303 was evaluated for functional activity in: 1) human lymphocyte assays, 2) the NOD.Aec1Aec2 spontaneous model of Sjogren’s syndrome (SjS), 3) the bm12-induced mouse model of lupus, 4) the (NZB/NZW)F1 spontaneous model of lupus, and 5) preclinical rodent and cynomolgus monkey pharmacokinetic/pharmacodynamic studies.Results:ALPN-303 inhibited BAFF- and APRIL-mediated signaling in vitro in human lymphocyte assays, with significantly lower IC50 values than WT TACI-Fc and belimumab comparators. In all mouse models evaluated, administration of ALPN-303 rapidly and significantly reduced key lymphocyte subsets including plasma cells, germinal center B cells, and follicular T helper cells. ALPN-303 significantly reduced autoantibodies and sialadenitis in the spontaneous SjS model, inhibited glomerular IgG deposition in the bm12-induced model of lupus, and potently suppressed anti-dsDNA autoAbs, blood urea nitrogen levels, proteinuria, sialadenitis, kidney lesions, and renal immune complex deposition in the NZB/W lupus model. As compared to WT TACI-Fc, ALPN-303 exhibited higher serum exposure and significantly and persistently decreased titers of serum IgM, IgG, and IgA antibodies in mice and cynomolgus monkeys (Figure 1).Figure 1.ALPN-303 induces more potent suppression, as compared to WT TACI-Fc, of serum immunoglobulins following a single 9 mg/kg IV infusion (on Day 0; arrows) in female cynomolgus monkeys.Conclusion:ALPN-303 is a potent BAFF/APRIL antagonist derived from our directed evolution platform that consistently demonstrates encouraging immunomodulatory activity and efficacy in vitro and in vivo, superior in preclinical studies to anti-BAFF antibody and WT TACI-Fc. This novel Fc fusion molecule demonstrates favorable preliminary developability characteristics, including higher serum exposures and more potent immunosuppressive activities, which may enable lower clinical doses and/or longer dosing intervals than WT TACI-Fc therapeutics. ALPN-303 may thus be an attractive development candidate for the treatment of multiple autoimmune and inflammatory diseases, particularly B cell-related diseases such as SLE, SjS, and other connective tissue diseases. Preclinical development is underway to enable the initiation of clinical trials later this year.Disclosure of Interests:Stacey R. Dillon Shareholder of: Alpine Immune Sciences, Bristol Myers Squibb, Employee of: Alpine Immune Sciences, Bristol Myers Squibb, Lawrence S. Evans Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Katherine E. Lewis Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Jing Yang Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Mark W. Rixon Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Joe Kuijper Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Dan Demonte Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Janhavi Bhandari Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Steve Levin Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Kayla Kleist Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Sherri Mudri Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Susan Bort Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Daniel Ardourel Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Michelle A. Seaberg Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Rachel Wang Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Chelsea Gudgeon Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Russell Sanderson Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Martin F. Wolfson Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Jan Hillson Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences, Stanford L. Peng Shareholder of: Alpine Immune Sciences, Employee of: Alpine Immune Sciences

To improve bycatch mitigation of chondrichthyans, reptiles and cetaceans for a tropical demersal fish-trawl fishery, species-specific responses to bycatch reduction devices (BRDs) were investigated using both in situ subsurface and onboard observations. There are few, if any, studies that have determined mitigation performances of BRDs from subsurface interactions for these species, as most are rarely encountered and thus require substantial levels of observer coverage for robust assessments. This study combined in-net and onboard (774 day trawls and 1320 day trawl hours of subsurface observer coverage) electronic monitoring on all fish-trawl vessels (n = 3) to compare bycatch mitigation performances among nine megafauna groups, based on escape rates and interaction durations for three BRDs over 6 months (June to December 2012). Overall, 26.9% of day trawls had no megafauna interactions and 38.3% of the 1826 interactions escaped, with most in rapid time (91.4% in ≤ 5 min). The upward inclined exclusion grid significantly improved the escape proportions for most chondrichthyans by 20–30%. All BRDs were highly effective in reducing reptile (turtles and seasnakes) bycatch, but irrelevant for the few sawfish (n = 13) that readily entangled in the anterior of the net. Cetacean (bottlenose dolphins only) interactions with BRDs were very rare (n = 7) despite high levels of attendance and depredation during trawling. Loss of targeted teleosts through the BRD hatch was rare (1.3% of day trawls). This relatively cost-effective method of electronic monitoring achieved very high levels of subsurface observer coverage (60% of day trawls or 56% of day trawl hours), and provided evidence that the subsurface expulsion of megafauna in poor condition is negligible. Furthermore, this study provides species-specific improvements toward bycatch mitigation strategies for demersal fish trawling.

Background Overexpression or administration of interleukin 31 (IL-31) has been shown to induce a profound itch response in mice and dogs. The chronic pruritus observed in mouse IL-31 transgenic mice results in the development of skin lesions and alopecia through excoriation from excessive scratching, a condition similar to that observed in patients with atopic dermatitis (AD). Objective To test whether IL-31 induces pruritus in non-human primates and, if so, whether treatment with an anti-IL-31 neutralizing monoclonal antibody (mAb) can block the response. Methods A series of studies was conducted in cynomolgus monkeys to evaluate the itch response to recombinant cynomolgus IL-31 (cIL-31) administration. Three routes of cIL-31 administration (intravenous, intradermal, and subcutaneous) were evaluated. Subcutaneous treatment with a humanized anti-human IL-31 mAb cross-reactive to cIL-31 was subsequently tested for its ability to block the response to intradermal cIL-31 administration. Results Each route of cIL-31 delivery elicited a scratching response immediately after cIL-31 administration and lasted at least 3 h. Treatment with the IL-31 mAb inhibited the cIL-31-mediated scratching response in a dose-dependent manner. Conclusion These results demonstrate that an IL-31 mAb can inhibit IL-31-mediated pruritus in vivo, and could be an effective therapy for pruritic skin conditions like AD where IL-31 upregulation may play a role.

The Sargasso Sea is a dynamic physical environment in which strong seasonal variability combines with forcing by mesoscale (~100 km) eddies. These drivers determine nutrient, light, and temperature regimes and, ultimately, the composition and productivity of the phytoplankton community. On four cruises (2011 and 2012; one eddy per cruise), we investigated links between water column structure and phytoplankton community composition in the Sargasso at a range of time and space scales. On all cruises, cyanobacteria ( Prochlorococcus and Synechococcus ) dominated the phytoplankton numerically, while haptophytes were the dominant eukaryotes (up to 60% of total chl- a ). There were substantial effects of mesoscale and sub-mesoscale forcing on phytoplankton community composition in both spring and summer. Downwelling (in anticyclones) resulted in Prochlorococcus abundances that were 22−66% higher than at ‘outside’ stations. Upwelling (in cyclones) was associated with significantly higher abundances and POC biomass of nanoeukaryotes. In general, however, each eddy had its own unique characteristics. The center of anticyclone AC1 (spring 2011) had the lowest phytoplankton biomass (chl- a ) of any eddy we studied and had lower nitrate+nitrite (N+N −2 ) and eukaryote chl- a biomass as compared to its edge and to the Bermuda Atlantic Time-Series station (BATS). At the center of cyclone C1 (summer 2011), we observed uplift of the 26.5 kg m −3 isopycnal and high nutrient inventories (N+N=74±46 mmol m −2 ). We also observed significantly higher haptophyte chl- a (non-coccolithophores) and lower cyanobacterial chl- a at the center and edge of C1 as compared to outside the eddy at BATS. Cyclone C2 (spring 2012) exhibited a deep mixed layer, yet had relatively low nutrient concentrations. We observed a shift in the taxonomic composition of haptophytes between a coccolithophore-dominated community in C2 (98% of total haptophyte chl- a ) and a non-coccolithophore community at BATS. In summer 2012, downwelling associated with anticyclone AC2 occurred at the edge of the eddy (not at the center), where AC2 interacted with a nearby cyclone. At the edge, we found significantly lower Synechococcus abundances and higher eukaryote chl- a compared to the center of AC2 and BATS. These along-transect nuances demonstrate the significance of small-scale perturbations that substantially alter phytoplankton community structure. Therefore, while seasonality in the North Atlantic is the primary driver of broad-scale trends in phytoplankton community composition, the effects of transient events must be considered when studying planktonic food webs and biogeochemical cycling in the Sargasso Sea.

Background:BAFF and APRIL are TNF superfamily members that bind both TACI and BCMA on B cells; BAFF also binds BAFF-R. Together, BAFF and APRIL support B cell development, differentiation, and survival. Their co-neutralization dramatically reduces B cell function, including antibody production, whereas inhibition of either BAFF or APRIL alone mediates relatively modest effects.Objectives:While CTLA-4-based therapeutics that block T cell costimulation provide safe and moderately effective T cell inhibition in many disease settings, and while B cell targeting therapies have demonstrated promising therapeutic potential, we postulate that improved, combined BAFF and APRIL inhibition, either alone or coupled with inhibition of T cell costimulation, will provide more effective and durable relief from severe B cell-related autoimmune diseases like SLE.Methods:We used our directed evolution platform to identify variant domains of the TNF family receptors TACI or BCMA that exhibit enhanced affinity for BAFF and APRIL as compared to their wild-type (WT) counterparts. These variant TACI or BCMA domains (vTD), alone or together with platform-derived CTLA-4 domains (vIgD), were fused to a modified human IgG1 Fc lacking effector function, yielding a panel of immunomodulatory molecules: TACI vTD-Fc, BCMA vTD-Fc, TACI vTD/CTLA-4 vIgD-Fc, & BCMA vTD/CTLA-4 vIgD-Fc. All were evaluated for functional activity: 1)in vitroin primary human B cell & MLR assays and in a Jurkat/NF-kB reporter cell line expressing TACI, and 2)in vivoin standard immunization models, and in the bm12-induced and NZB/NZW spontaneous mouse models of lupus.Results:The novel engineered TACI vTD-Fc or BCMA vTD-Fc fusion proteins significantly inhibited BAFF- and APRIL-mediated signalingin vitroin TACI+Jurkat cells. TACI (or BCMA) vTD/CTLA-4 vIgD-Fc proteins also attenuated T cell activation in primary human lymphocyte assays. When administered to mice, these molecules rapidly and potently reduced key B and T cell subsets, including plasma cells, follicular T helper cells, germinal center cells, & memory T cells. Treatment with TACI vTD-Fc or TACI vTD/CTLA-4 vIgD-Fc proteins also significantly reduced titers of antigen-specific antibodies in immunized mice more so than abatacept or WT TACI-Fc, and potently suppressed anti-dsDNA autoantibodies, blood urea nitrogen levels, proteinuria, and renal immune complex deposition in the bm12 & NZB/W lupus models.Conclusion:Directed evolution of TNFR and IgSF domains has successfully facilitated the development of Fc fusion proteins containing TACI or BCMA vTDs, with or without fusion to CTLA-4 vIgDs. These novel immunomodulators consistently demonstrate potent immunosuppressive activity and efficacyin vitroandin vivo, appearing superior to existing and/or approved immunomodulators like belimumab, abatacept, or atacicept. Such biologics may therefore be attractive candidates for the treatment of serious autoimmune diseases, particularly B cell-related diseases such as SLE, Sjogren’s syndrome, etc.Disclosure of Interests: :Stacey R. Dillon Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Lawrence S. Evans Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Mark W. Rixon Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Joe Kuijper Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Dan Demonte Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Katherine E. Lewis Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Steve Levin Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Kayla Kleist Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Sherri Mudri Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Susan Bort Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Janhavi Bhandari Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Fariha Ahmed-Qadri Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Jing Yang Shareholder of: Alpine Immune Sciences, Inc., Employee of: Alpine Immune Sciences, Inc., Michelle A. Seaberg Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Rachel Wang Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Russell Sanderson Shareholder of: Alpine Immune Sciences, Inc., Employee of: Alpine Immune Sciences, Inc., Martin F. Wolfson Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Jan Hillson Shareholder of: Alpine Immune Sciences, Inc., Employee of: Alpine Immune Sciences, Inc., Stanford L. Peng Shareholder of: Alpine Immune Sciences, Inc., Employee of: CMO and President of Alpine Immune Sciences, Inc., Kristine M. Swiderek Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc.

Gene expression in a tissue-specific context depends on the combined efforts of epigenetic, transcriptional and post-transcriptional processes that lead to the production of specific proteins that are important determinants of cellular identity. Ribosomes are a central component of the protein biosynthesis machinery in cells; however, their regulatory roles in the translational control of gene expression in skeletal muscle remain to be defined. In a genetic screen to identify critical regulators of myogenesis, we identified a DEAD-Box RNA helicase, DDX27, that is required for skeletal muscle growth and regeneration. We demonstrate that DDX27 regulates ribosomal RNA (rRNA) maturation, and thereby the ribosome biogenesis and the translation of specific transcripts during myogenesis. These findings provide insight into the translational regulation of gene expression in myogenesis and suggest novel functions for ribosomes in regulating gene expression in skeletal muscles., Author summary Inherited skeletal muscle diseases are the most common form of genetic disorders with primary abnormalities in the structure and function of skeletal muscle resulting in the impaired locomotion in affected patients. A major hindrance to the development of effective therapies is a lack of understanding of biological processes that promote skeletal muscle growth. By performing a forward genetic screen in zebrafish we have identified mutation in a RNA helicase that leads to perturbations of ribosomal biogenesis pathway and impairs skeletal muscle growth and regeneration. Therefore, our studies have identified novel ribosome-based disease processes that may be therapeutic modulated to restore muscle function in skeletal muscle diseases.

Although awareness of familial hypercholesterolemia (FH) is increasing, this common, potentially fatal, treatable condition remains underdiagnosed. Despite FH being a genetic disorder, genetic testing is rarely used. The Familial Hypercholesterolemia Foundation convened an international expert panel to assess the utility of FH genetic testing. The rationale includes the following: 1) facilitation of definitive diagnosis; 2) pathogenic variants indicate higher cardiovascular risk, which indicates the potential need for more aggressive lipid lowering; 3) increase in initiation of and adherence to therapy; and 4) cascade testing of at-risk relatives. The Expert Consensus Panel recommends that FH genetic testing become the standard of care for patients with definite or probable FH, as well as for their at-risk relatives. Testing should include the genes encoding the low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin 9 (PCSK9); other genes may also need to be considered for analysis based on patient phenotype. Expected outcomes include greater diagnoses, more effective cascade testing, initiation of therapies at earlier ages, and more accurate risk stratification.

Recent advances in cancer treatment with checkpoint blockade of receptors such as CTLA-4 and PD-1 have demonstrated that combinations of agents with complementary immunomodulatory effects have the potential to enhance antitumor activity as compared to single agents. We investigated the efficacy of immune-modulatory interleukin-21 (IL-21) combined with checkpoint blockade in several syngeneic mouse tumor models. After tumor establishment, mice were administered recombinant mouse IL-21 (mIL-21) alone or in combination with blocking monoclonal antibodies against mouse PD-1 or CTLA-4. In contrast to monotherapy, IL-21 enhanced antitumor activity of mCTLA-4 mAb in four models and anti-PD-1 mAb in two models, with evidence of synergy for one or both of the combination treatments in the EMT-6 and MC38 models. The enhanced efficacy was associated with increased intratumoral CD8+ T cell infiltrates, CD8+ T cell proliferation, and increased effector memory T cells, along with decreased frequency of central memory CD8+ T cells. In vivo depletion of CD8+ T cells abolished the antitumor activities observed for both combination and monotherapy treatments, further supporting a beneficial role for CD8+ T cells. In all studies, the combination therapies were well tolerated. These results support the hypothesis that the combination of recombinant human IL-21 with CTLA-4 or PD-1 monoclonal antibodies could lead to improved outcomes in cancer patients.

Allomaternal care (AMC) (i.e., infant care that is provided by group members other than an infant's mother) is a rare, although phylogenetically widespread, mammalian infant care strategy. In primates, however, AMC occurs at unusually high frequencies, particularly among several haplorhine (monkey and ape) taxa. In fact, AMC is present in every major primate radiation and has been described in 74% of 154 species for which data are available. Its widespread presence in the Order Primates suggests that there may have been strong selective pressure for AMC early in primate evolution, but it is currently unknown why these behaviors are so common in primates. Research focused on captive callitrichids (tamarins and marmosets) has contributed greatly to our understanding of the potential causes and consequences of highly derived forms of AMC (i.e., cooperative breeding). Recent efforts have shifted focus to understand the selective pressures leading to the expansion and diversification of AMC throughout the Primate Order, thus expanding research to investigate the causes and consequences of less derived forms of AMC. Here we review the broad-scale patterns observed in primates and outline innovative and exciting avenues of research moving forward. Keywords: infant care; allomother; helper; hormones; behavioral genetics

Background Genomic profiling of lesional and nonlesional skin of patients with atopic dermatitis (AD) using microarrays has led to increased understanding of AD and identification of novel therapeutic targets. However, the limitations of microarrays might decrease detection of AD genes. These limitations might be lessened with next-generation RNA sequencing (RNA-seq). Objective We sought to define the lesional AD transcriptome using RNA-seq and compare it using microarrays performed on the same cohort. Methods RNA-seq and microarrays were performed to identify differentially expressed genes (criteria: fold change, ≥2.0; false discovery rate ≤0.05) in lesional versus nonlesional skin from 18 patients with moderate-to-severe AD, with real-time PCR (RT-PCR) and immunohistochemistry used for validation. Results Both platforms showed robust disease transcriptomes and correlated well with RT-PCR. The common AD transcriptome identified by using both techniques contained 217 genes, including inflammatory ( S100A8/A9/A12, CXCL1 , and 2′-5′-oligoadenylate synthetase-like [ OASL ]) and barrier ( MKi67 , keratin 16 [ K16 ], and claudin 8 [ CLDN8 ]) AD-related genes. Although fold change estimates determined by using RNA-seq showed somewhat better agreement with RT-PCR (intraclass correlation coefficient, 0.57 and 0.70 for microarrays and RNA-seq vs RT-PCR, respectively), bias was not eliminated. Among genes uniquely identified by using RNA-seq were triggering receptor expressed on myeloid cells 1 (TREM-1) signaling (eg, CCL2 , CCL3 , and single immunoglobulin domain IL1R1 related [ SIGIRR ]) and IL-36 isoform genes. TREM-1 is a surface receptor implicated in innate and adaptive immunity that amplifies infection-related inflammation. Conclusions This is the first report of a lesional AD phenotype using RNA-seq and the first direct comparison between platforms in this disease. Both platforms robustly characterize the AD transcriptome. Through RNA-seq, we unraveled novel disease pathology, including increased expression of the novel TREM-1 pathway and the IL-36 cytokine in patients with AD.

Interleukin 31 receptor α (IL-31RA) is a novel Type I cytokine receptor that pairs with oncostatin M receptor to mediate IL-31 signaling. Binding of IL-31 to its receptor results in the phosphorylation and activation of STATs, MAPK, and JNK signaling pathways. IL-31 plays a pathogenic role in tissue inflammation, particularly in allergic diseases. Recent studies demonstrate IL-31RA expression and signaling in non-hematopoietic cells, but this receptor is poorly studied in immune cells. Macrophages are key immune-effector cells that play a critical role in Th2-cytokine-mediated allergic diseases. Here, we demonstrate that Th2 cytokines IL-4 and IL-13 are capable of up-regulating IL-31RA expression on both peritoneal and bone marrow-derived macrophages from mice. Our data also demonstrate that IL-4Rα-driven IL-31RA expression is STAT6 dependent in macrophages. Notably, the inflammation-associated genes Fizz1 and serum amyloid A (SAA) are significantly up-regulated in M2 macrophages stimulated with IL-31, but not in IL-4 receptor-deficient macrophages. Furthermore, the absence of Type II IL-4 receptor signaling is sufficient to attenuate the expression of IL-31RA in vivo during allergic asthma induced by soluble egg antigen, which may suggest a role for IL-31 signaling in Th2 cytokine-driven inflammation and allergic responses. Our study reveals an important counter-regulatory role between Th2 cytokine and IL-31 signaling involved in allergic diseases. Background: IL-31RA is a novel Type I cytokine receptor that pairs with oncostatin M receptor to mediate IL-31 signaling. Results: Th2 cytokines up-regulate IL-31RA signaling in macrophages. Conclusion: We demonstrate that the Th2 cytokines IL-4 and IL-13 were capable of up-regulating IL-31RA expression on macrophages. Significance: This newly identified counter-regulatory role between Th2 cytokine and the IL-31 signaling cascade may provide valuable insights into the pathobiology of allergic diseases.

Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying transcription factors (TFs) involved in a specific process and used it to map regulation of the key virulence factor of a deadly fungus—its capsule. The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, midlevel, and “foreman” TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. These resources and analyses provide the first integrated, systems-level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to laboratories focused on specific physiological processes.

Animal behaviours, like aggression, can directly affect host health by influencing exposure to parasites. Aggressive individuals may experience an increase in agonistic interactions and contact rates with conspecifics, which might increase their probability of acquiring parasites. However, aggression is not the only factor that shapes parasitism; proximate mechanisms like hormone-modulated immunosuppression can also have broad impacts. Here, we hypothesized that high levels of aggression, cortisol and testosterone would be positively associated with parasitism and that aggressive individuals would play a larger role spreading parasites to conspecifics than would docile individuals. We measured aggression using the level of aggressive response to human handling during capture. Our aim was to examine associations between aggression and hormones (cortisol and testosterone) on variation in endo- and ectoparasitism in a population of wild mouse lemurs ( Microcebus rufus ) over a 3-year period. By tracking the movement of lice (directly transmitted parasites) in the population, we also examined the effect of host aggression on population-wide parasite dynamics. We show that animals with high testosterone and cortisol were more likely to exhibit aggressive behaviours, and cortisol was associated with significantly higher ectoparasite infestations. Aggressive individuals were significantly more infested by lice, and also donated significantly more lice to conspecifics in the population. Taken together, our results offer insight into the individual and population health costs of aggression, and empirical support of a trade-off between aggression and ectoparasitism, which may have driven the evolution of aggression and interactions with conspecifics.

Over the past decade several studies have reported that the gut microbiomes of mammals with similar dietary niches exhibit similar compositional and functional traits. However, these studies rely heavily on samples from captive individuals and often confound host phylogeny, gut morphology, and diet. To more explicitly test the influence of host dietary niche on the mammalian gut microbiome we use 16S rRNA gene amplicon sequencing and shotgun metagenomics to compare the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely related non-folivores, evenly distributed throughout the primate order and representing a range of gut morphological specializations. While folivory results in some convergent microbial traits, collectively we show that the influence of host phylogeny on both gut microbial composition and function is much stronger than that of host dietary niche. This pattern does not result from differences in host geographic location or actual dietary intake at the time of sampling, but instead appears to result from differences in host physiology. These findings indicate that mammalian gut microbiome plasticity in response to dietary shifts over both the lifespan of an individual host and the evolutionary history of a given host species is constrained by host physiological evolution. Therefore, the gut microbiome cannot be considered separately from host physiology when describing host nutritional strategies and the emergence of host dietary niches.

Animals with dietary specializations can be used to link climate to specific ecological drivers of endangerment. Only two mammals, the giant panda (Ailuropoda melanoleuca) in Asia and the greater bamboo lemur (Prolemur simus) in Madagascar, consume the nutritionally poor and mechanically challenging culm or trunk of woody bamboos [1-3]. Even though the greater bamboo lemur is critically endangered, paleontological evidence shows that it was once broadly distributed [4, 5]. Here, integrating morphological, paleontological, and ecological evidence, we project the effects of climate change on greater bamboo lemurs. Both the giant panda and the greater bamboo lemur are shown to share diagnostic dental features indicative of a bamboo diet, thereby providing an ecometric indicator [6, 7] of diet preserved in the fossil record. Analyses of bamboo feeding in living populations show that bamboo culm is consumed only during the dry season and that the greater bamboo lemur is currently found in regions with the shortest dry season. In contrast, paleontological localities of the greater bamboo lemurs have the longest dry seasons. Future projections show that many present-day greater bamboo lemur populations will experience prolonged dry seasons similar to those of the localities where only fossils of the greater bamboo lemur are found. Whereas abundant foods such as bamboo allow feeding specialists to thrive, even a moderate change in seasonality may outstrip the capacity of greater bamboo lemurs to persist on their mechanically demanding food source. Coupling known changes in species distribution with high-resolution ecological and historical data helps to identify extinction risks.

Neuroendocrine evidence suggests that paternal care is mediated by hormonal mechanisms, where hormonal changes in expectant and new fathers facilitate infant care. In species with obligate and extensive paternal care such as humans, androgen levels decline once males are paired and have offspring, and in direct response to offspring care. Facultative infant care is widespread in the Order Primates, but the underlying hormonal mechanisms are largely unknown. We found that wild, red-bellied lemurs living in family groups (two adults and their presumed offspring) varied in the amount of care they provided infants. The more fathers invested in helping infants (measured as a composite of carrying, holding, huddling, grooming, and playing), and specifically the more they huddled and groomed with infants, the higher their fecal androgen (fA) levels, contrary to expectations. Carrying was negatively related to fA levels. Helping by subadults and juveniles was not related to their own fA levels. Elevated fA levels during infant dependence have been observed in other vertebrate species, and are thought to reflect reinvestment in mating rather than investment in dependent offspring. However, red-bellied lemurs do not mate until after infants are weaned, and they have long-term pair-bonds, suggesting that elevated fA levels play a role in offspring care. These results support a growing body of research suggesting that elevated androgen levels do not inhibit protective infant care.

Background Increased airway smooth muscle is observed in large and small airways in asthma. Semi-quantitative estimates suggest that cells containing alpha smooth muscle actin (α-SMA) are also increased in the lung parenchyma. This study quantified and characterized α-SMA positive cells (α-SMA+) in the lung parenchyma of non-asthmatic and asthmatic individuals. Methods Post-mortem sections of peripheral lung from cases of fatal asthma (FA), persons with asthma dying of non-respiratory causes (NFA) and non-asthma control subjects (NAC) were stained for α-SMA, quantified using point-counting and normalised to alveolar basement membrane length and interstitial area. Results α-SMA+ fractional area was increased in alveolar parenchyma in both FA (14.7 ± 2.8% of tissue area) and NFA (13.0 ± 1.2%), compared with NAC (7.4 ± 2.4%), p < 0.05 The difference was greater in upper lobes compared with lower lobes (p < 0.01) in both asthma groups. Similar changes were observed in alveolar ducts and alveolar walls. The electron microscopic features of the α-SMA+ cells were characteristic of myofibroblasts. Conclusions We conclude that in asthma there is a marked increase in α-SMA+ myofibroblasts in the lung parenchyma. The physiologic consequences of this increase are unknown.

The behavior of three antibiotics (bacitracin, chlortetracycline, and tylosin) and two classes of antibiotic resistance genes (ARGs), tet and erm, were monitored in swine manure slurry under anaerobic conditions. First-order decay rates were determined for each antibiotic with half-lives ranging from 1 day (chlortetracycline) to 10 days (tylosin). ARGs were monitored in the swine manure slurry, and losses of approximately 1 to 3 orders of magnitude in relative abundance were observed during the 40 day storage period. First-order degradation profiles were observed for chlortetracycline and its corresponding resistance genes, tet(X) and tet(Q). Tylosin was degraded to approximately 10% of the starting concentration by day 40; however, the relative abundance of erm(B) remained at 50-60% of the initial relative abundance while the relative abundance of erm(F) decreased by 80-90%, consistent with tylosin. These results indicate that tet resistance genes respond primarily to chlortetracycline antimicrobials, and may be lost when the parent tetracycline compound is degraded. In contrast, erm(B) resistance gene may respond to a range of antimicrobials in animal manure, and may persist despite losses of tylosin.

Objective To investigate the distribution of retinal ganglion cells (RGCs) and visual acuity in alpacas (Vicugna pacos) through Brn-3a immunofluorescent labeling. Procedures Five eyes from four healthy alpacas with normal ophthalmic examination findings were included in the study. The axial length of the globes was measured before fixation. All five retinas were treated with Brn-3a antibodies to label RGCs. Images taken with a fluorescent microscope were used for RGC counting. RGC density maps were reconstructed by computer software. Visual acuity was estimated based on the results of peak RGC density and ocular anatomical parameters. Results The reconstructed retinal maps from Brn-3a labeling showed a horizontal streak across the retinal meridian superior to the optic nerve head with a temporal, upward extension. The highest RGC densities were in the temporal retinas. The maximal visual acuity was located in the temporal retina and was estimated to range between 12.5 and 13.4 cycles per degree. Conclusions Alpacas have a horizontal streak across the retinal meridian superior to the optic disk with a temporal, upward extension based on the Brn-3a labeling of RGCs. The maximal visual acuity was located in the temporal retina. The reconstructed retinal maps indicate the RGC topography of alpacas is similar to that of other herbivores, but is different from that of dromedary camels.

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in CELLULASE3/GLYCOSYLHYDROLASE9B3 and LEUCINE RICH EXTENSIN2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.

As short tandem repeat markers remain the foundation of human identification throughout the world, new STR multiplexes require rigorous testing to ensure the assays are sufficiently robust and reliable for genotyping purposes. The PowerPlex ® 18D System was created for the direct amplification of buccal and blood samples from FTA ® storage cards and reliably accommodates other sample materials. The PowerPlex ® 18D System allows simultaneous amplification of the 13 CODIS loci and amelogenin along with four additional loci: Penta E, Penta D, D2S1338, and D19S433. To demonstrate suitability for human identification testing, the PowerPlex ® 18D System was tested for sensitivity, concordance, inhibitor tolerance, and performance with thermal cycling and reaction condition variation following SWGDAM developmental validation guidelines. Given these results, PowerPlex ® 18D System can confidently be used for forensic and human identification testing.

Sexually selected traits and the use of strategies to enhance male reproductive success (e.g., competition and dispersal) can yield sex differences in metabolic requirements, rates and durations of growth and maturation, and the propensity for risky behavior, which are suggested to result in age-specific sex differences in mortality and life span. We investigated age-specific sex ratios, mortality, and dispersal in Propithecus edwardsi in Ranomafana National Park, Madagascar. We predicted that, due to similarities in growth rates and body sizes, male and female juvenile mortality rates would be comparable; because both sexes disperse and have intense intersexual competition and aggression, adult mortality would be similar; given similarities in dispersal frequency and distance, the timing of dispersal would not differ. We used 80 group-years births, deaths, and dispersals (N females = 41, N males = 34) collected over 23 years to calculate sex ratios and survival curves. Females lived longer than males (maximum 32 and 19 years, respectively). Sex ratios were male biased from sexual maturity through 17 years and female biased at birth and older ages. Infant survival probabilities were similar. Thus, differential development and maturation are unlikely explanations for longer female life span in this species. Males were more likely to survive from 2 to 18 years. However, male annual survival probability declined quickly around 13–18 years; males continued to disperse until their deaths, whereas females generally stopped dispersing after 11 years. We suggest that sex differences in the timing of dispersal and the unique challenges of risky behavior at older ages may be sufficient to yield differences in male and female life span.

The ability to rationally manipulate the transcriptional states of cells would be of great use in medicine and bioengineering. We have developed an algorithm, NetSurgeon, which uses genome-wide gene-regulatory networks to identify interventions that force a cell toward a desired expression state. We first validated NetSurgeon extensively on existing datasets. Next, we used NetSurgeon to select transcription factor deletions aimed at improving ethanol production in Saccharomyces cerevisiae cultures that are catabolizing xylose. We reasoned that interventions that move the transcriptional state of cells using xylose toward that of cells producing large amounts of ethanol from glucose might improve xylose fermentation. Some of the interventions selected by NetSurgeon successfully promoted a fermentative transcriptional state in the absence of glucose, resulting in strains with a 2.7-fold increase in xylose import rates, a 4-fold improvement in xylose integration into central carbon metabolism, or a 1.3-fold increase in ethanol production rate. We conclude by presenting an integrated model of transcriptional regulation and metabolic flux that will enable future efforts aimed at improving xylose fermentation to prioritize functional regulators of central carbon metabolism.

Cryptococcus neoformans is a ubiquitous, opportunistic fungal pathogen that kills over 600,000 people annually. Here, we report integrated computational and experimental investigations of the role and mechanisms of transcriptional regulation in cryptococcal infection. Major cryptococcal virulence traits include melanin production and the development of a large polysaccharide capsule upon host entry; shed capsule polysaccharides also impair host defenses. We found that both transcription and translation are required for capsule growth and that Usv101 is a master regulator of pathogenesis, regulating melanin production, capsule growth, and capsule shedding. It does this by directly regulating genes encoding glycoactive enzymes and genes encoding three other transcription factors that are essential for capsule growth: GAT201, RIM101, and SP1. Murine infection with cryptococci lacking Usv101 significantly alters the kinetics and pathogenesis of disease, with extended survival and, unexpectedly, death by pneumonia rather than meningitis. Our approaches and findings will inform studies of other pathogenic microbes., IMPORTANCE Cryptococcus neoformans causes fatal meningitis in immunocompromised individuals, mainly HIV positive, killing over 600,000 each year. A unique feature of this yeast, which makes it particularly virulent, is its polysaccharide capsule; this structure impedes host efforts to combat infection. Capsule size and structure respond to environmental conditions, such as those encountered in an infected host. We have combined computational and experimental tools to elucidate capsule regulation, which we show primarily occurs at the transcriptional level. We also demonstrate that loss of a novel transcription factor alters virulence factor expression and host cell interactions, changing the lethal condition from meningitis to pneumonia with an exacerbated host response. We further demonstrate the relevant targets of regulation and kinetically map key regulatory and host interactions. Our work elucidates mechanisms of capsule regulation, provides methods and resources to the research community, and demonstrates an altered pathogenic outcome that resembles some human conditions.

Recent evidence indicates that extracellular nucleotides regulate plant growth. Exogenous ATP has been shown to block auxin transport and gravitropic growth in primary roots of Arabidopsis (Arabidopsis thaliana). Cells limit the concentration of extracellular ATP in part through the activity of ectoapyrases (ectonucleoside triphosphate diphosphohydrolases), and two nearly identical Arabidopsis apyrases, APY1 and APY2, appear to share this function. These findings, plus the fact that suppression of APY1 and APY2 blocks growth in Arabidopsis, suggested that the expression of these apyrases could influence auxin transport. This report tests that hypothesis. The polar movement of [3H]indole-3-acetic acid in both hypocotyl sections and primary roots of Arabidopsis seedlings was measured. In both tissues, polar auxin transport was significantly reduced in apy2 null mutants when they were induced by estradiol to suppress the expression of APY1 by RNA interference. In the hypocotyl assays, the basal halves of APY-suppressed hypocotyls contained considerably lower free indole-3-acetic acid levels when compared with wild-type plants, and disrupted auxin transport in the APY-suppressed roots was reflected by their significant morphological abnormalities. When a green fluorescent protein fluorescence signal encoded by a DR5:green fluorescent protein construct was measured in primary roots whose apyrase expression was suppressed either genetically or chemically, the roots showed no signal asymmetry following gravistimulation, and both their growth and gravitropic curvature were inhibited. Chemicals that suppress apyrase activity also inhibit gravitropic curvature and, to a lesser extent, growth. Taken together, these results indicate that a critical step connecting apyrase suppression to growth suppression is the inhibition of polar auxin transport.

Diel variation is known to alter the composition and structure of reef fish assemblages. What is unknown is how nocturnal fish assemblages respond to closed fishery area management. Diurnal and nocturnal reef fish assemblages at the Houtman Abrolhos Islands, Western Australia, were studied using baited remote underwater stereo-video systems (stereo-BRUVs). Surveys were conducted during the day and at night (using blue illumination) from three sites inside and three sites outside a closed fishery area (CFA). The relative abundance of 116 fish species from 41 families was recorded. Significant changes were observed in fish assemblage structure from day to night (driven by high dispersion at night) and in areas open versus closed to fishing (driven by increased abundance within the CFA). The effect of protection from fishing was consistent for both diurnal and nocturnal fish assemblages. Closer examination of six targeted fish species showed that their response to diel changes and the absence of fishing pressure varied from species to species. The targeted fishes Pagrus auratus and Glaucosoma hebraicum were sampled during the day and at night with both species responding positively to protection from fishing. Results suggest that the inclusion of diurnal and nocturnal fish assemblage data will provide an improved ability to assess the effectiveness of closed fishery area management.

Allomaternal care is a rare, though phylogenetically widespread, mammalian infant care strategy. Among primates, the effects of allomaternal care are marked; its presence correlates with faster infant growth, younger age at weaning, and shorter interbirth intervals. Recent comparative research has found that such fertility benefits are absent in other mammals and are thus unique to primates. In large part because data describing lemur allomaternal care were lacking, the reproductive advantages of allomaternal care have never been demonstrated in Malagasy strepsirrhines. Using newly available data and rigorous phylogenetic methods, we extend this hypothesis to strepsirrhines and test whether allomaternal care in lemurs confers similar maternal reproductive benefits. Contrary to expectations, the presence of allomaternal care did not significantly impact lemur reproductive output; we did not find relationships between allomaternal care and either fetal or postnatal growth rates or interbirth intervals. Rather, infant parking and nesting, strategies employed primarily by litter-bearing species, were positively associated with faster fetal and postnatal infant growth, while nesting was negatively associated with interbirth interval. Thus, although each form of haplorrhine allomaternal care is also observed in Malagasy primates, the effects that these behaviors have on female reproductive output more closely resemble nonprimate mammals. We suggest that Malagasy strepsirrhines may not equally benefit from allomaternal care compared to haplorrhines because reproductive rates are less flexible and allomaternal care may instead increase infant survival in Madagascar’s harsh and unpredictable environment. Our study has significant implications for understanding the evolution of infant care and developmental trajectories in mammals.

Chronic lymphocytic leukemia (CLL) is a clonal B cell disorder of unknown origin. Accessory signals from the microenvironment are critical for the survival, expansion, and progression of malignant B cells. We found that the CLL stroma included microvascular endothelial cells (MVECs) expressing BAFF and APRIL, two TNF family members related to the T cell-associated B cell-stimulating molecule CD40L. Constitutive release of soluble BAFF and APRIL increased upon engagement of CD40 on MVECs by CD40L aberrantly expressed on CLL cells. In addition to enhancing MVEC expression of CD40, leukemic CD40L induced cleavases that elicited intracellular processing of pro-BAFF and pro-APRIL proteins in MVECs. The resulting soluble BAFF and APRIL proteins delivered survival, activation, Ig gene remodeling, and differentiation signals by stimulating CLL cells through TACI, BAFF-R, and BCMA receptors. BAFF and APRIL further amplified CLL cell survival by upregulating the expression of leukemic CD40L. Inhibition of TACI, BCMA, and BAFF-R expression on CLL cells; abrogation of CD40 expression in MVECs; or suppression of BAFF and APRIL cleavases in MVECs reduced the survival and diversification of malignant B cells. These data indicate that BAFF, APRIL, and CD40L form a CLL-enhancing bidirectional signaling network linking neoplastic B cells with the microvascular stroma.

For gregarious species, individuals must maintain cohesion while minimizing the costs of coordinated travel. Leaders of group movements potentially influence energy expenditure, energy intake, and predation risk for individuals in the group, which can have important fitness consequences. Models of pair-living species predict that energetic asymmetries lead to an emergent leader, with those in greater need leading. We investigated sex differences in leadership in pairs of red-bellied lemurs, Eulemur rubriventer, a monomorphic species with bisexual dispersal and no discernible hierarchy, to determine whether higher energetic requirements by adult females lead to female leadership. We collected leadership data in Ranomafana National Park, Madagascar on six groups of habituated E. rubriventer for 13 consecutive months between 2004–2005. To determine whether females led group movements more than males, we examined the difference in leadership frequencies of progressions in adult males and adult females within each group (n = 1,346 progressions). We further investigated the behavioral context (i.e. travel followed by feeding or not) and seasonal contexts (fruit availability, reproduction) of leadership. Group leadership was distributed, with different individuals leading the group at different times. However, females led significantly more than males, a pattern which was consistent in both feeding and non-feeding contexts and throughout all fruiting seasons and reproductive stages. While disparities in energetic status among the sexes may impact leadership in this species, leadership did not differ with changes in food availability or reproductive stage, and thus we were unable to determine whether female leadership might be related to changes in energetic status. Females may have higher energetic needs than males at all times, not merely seasonally, or female leadership may be unrelated to immediate energetic need. Rather, female leadership may be a legacy of female dominance not currently expressed in other contexts. Am. J. Primatol. 74:591–601, 2012. © 2012 Wiley Periodicals, Inc.