bluuebunny/crossref_metadata_2025 huggingface dataset:
The missing segment of the autopod 1st ray: new insights from a morphometric study of the human hand
Authors: Pazzaglia Ugo E. , Sibilia Valeria , Casati Lavinia , Salvi Andrea G. , Minini Andrea , Reguzzoni Marcella
Published: October 2018

Whether the 1st segment of the human autopod 1st ray is a ‘true’ metapodial with loss of the proximal or mid phalanx or the original basal phalanx with loss of the metacarpal has been a long‐lasting discussion. The actual knowledge of the developmental pattern of upper autopod segments at a fetal age of 20–22 weeks, combined with X‐ray morphometry of normal long bones of the hand in the growing ages, was used for analysis of the parameters, percentage length, position of epiphyseal ossification centers and proximal/distal growth rate. The symmetric growth pattern in the fetal anlagen changed to unidirectional in the postnatal development in relation to epiphyseal ossification formation. The percentage length assessment, the distribution of the epiphyseal ossification centers, and differential proximal/distal growth rate among the growing hand segments supported homology of most proximal segment of the thumb with the 2nd–5th proximal phalanges and that of the proximal phalanx of the thumb with the 2nd–5th mid phalanges in the same hand. Published case reports of either metanalysis of ‘triphalangeal thumb’ and ‘proximal/distal epiphyseal ossification centers’ were used to support the applied morphometric methodology; in particular, the latter did not give evidence of growth pattern inversion of the proximal segment of the thumb. The presented data support the hypothesis that during evolution, the lost segment of the autopod 1st ray is the metacarpal.
Impact of comorbidity on disease characteristics, treatment intent and outcome in diffuse large B‐cell lymphoma: a Swedish lymphoma register study
Authors: Wästerlid T. , Mohammadi M. , Smedby K. E. , Glimelius I. , Jerkeman M. , Bottai M. , Eloranta S.
Published: October 2018

Background

Comorbidity impacts overall survival amongst patients with diffuse large B‐cell lymphoma (DLBCL). However, associations of comorbidity with lymphoma characteristics, treatment selection and lymphoma‐specific mortality are less well known.

Objective

To examine the impact of comorbidity on DLBCL characteristics, treatment intent and cause of death.

Methods

We identified 3905 adult patients diagnosed with DLBCL 2007–2013 through the Swedish Lymphoma Register. We assessed comorbid disease history according to the Charlson comorbidity index (CCI). Comorbidity data and causes of death were collected through register linkage. Associations were estimated using multinomial regression and flexible parametric survival models.

Results

Overall, 45% of the patients (n = 1737) had a history of at least one comorbidity at DLBCL diagnosis (cardiovascular disease, diabetes and solid cancer were most frequent), and 997 (26%) had a CCI score of ≥2. The relative probability of presenting with poor performance status (PS > 2) was higher amongst comorbid patients [Relative Risk Ratio (RRR)PS>2: 2.02, 95% CI: 1.63–2.51]. Comorbid patients had a substantially lower relative probability of receiving curative treatment (RRR: 0.48, 95% CI: 0.38–0.61). Amongst all patients, CCI ≥ 1 was associated with a significantly increased risk of all‐cause and lymphoma‐specific death after adjustments. Amongst patients selected for curative treatment, comorbidity was associated with an increased risk of all‐cause death (HRCCI>1: 1.54, 95% CI: 1.32–1.80), but not with lymphoma‐specific death (HRCCI>1: 1.05, 95% CI: 0.86–1.28).

Conclusion

Comorbidity is associated with inferior DLBCL outcome, mainly due to a lower likelihood of receiving treatment with curative intent. Possibly, more comorbid DLBCL patients could be treated with curative intent if comorbid conditions were optimized in parallel.
Harried and Unhealthy? Parenthood, Time Pressure, and Mental Health
Authors: Ruppanner Leah , Perales Francisco , Baxter Janeen
Published: October 2018

Objective: This study investigates the effects of first and second births on time pressure and mental health and how these vary with time since birth and parental responsibilities. It also examines whether time pressure mediates the relationship between parenthood and mental health.

Background: Childbirth is a major life course transition that adds a new role to parents' role set and contributes to role strain, of which time pressure is one manifestation. Longitudinal analyses can help determine whether the impact of children on parental time pressure endures or eases over time and whether any changes affect parents' mental health.

Method: This study uses 16 years of panel data from the Household, Income and Labour Dynamics in Australia Survey (n = 20,009 individuals). The data are modeled using fixed effects panel regression models.

Results: First and second births increase time pressure to a similar extent. Their estimated effects are larger for women than men and persist over time, but there is limited evidence of moderation by parental responsibilities. Maternal mental health improves after a first child, whereas second children are associated with declines in paternal mental health. These effects are long lasting. Mediation analyses suggest that in the absence of time pressure maternal mental health would improve significantly.

Conclusion: Children have a stronger effect on mothers' than fathers' experiences of time pressure. These differences are not moderated by changes in parental responsibilities or work time following births. The increased time pressure associated with second births explains mothers' worse mental health.

Implications Parenthood is an important factor underpinning gendered experiences of time pressure. Reducing time pressure among parents may improve parental mental health, particularly among mothers.
Long‐term ingestion of low amylose/amylopectin ratio diet affects aspects of meat quality by changing muscle fibre characteristics in growing‐finishing pigs
Authors: Yang Can , He Jun , Yu Bing , Chen Daiwen , Mao XiangBing , Yu Jie , Yin Yulong
Published: October 2018

Amylose plays important role in body health. It is controversial whether changing dietary amylose/amylopectin ratio (DAR) will improve meat quality in growing‐finishing pigs. A total of 48 Duroc × Landrace × Large White castrated male pigs (initial body weight 49.8 ± 2.8 kg) were randomly allotted to two treatments, and fed ad libitum either with a low DAR diet (LR, amylose/amylopectin: 12/88) or a high DAR diet (HR, amylose/amylopectin: 30/70) for 68 days. Feed intake was recorded every day, body weight was weighed at 46th and 68th day to calculate average daily gain (ADG), average daily feed intake (ADFI) and Feed:gain ratio. Blood was collected at −30 min (fasting 12 hr), 60, 90, 120, 180 min postprandial at 64th day and then serum was obtained by centrifugation of blood at 1,500× g at 4°C. After pigs were slaughtered, samples such as longissimus dorsi, iliopsoas and semitendinosus were collected. Density, diameter and types of muscle fibres were analysed. Results showed that ADG, ADFI, Feed:Gain ratio, cross‐sectional area of longissimus dorsi muscle, backfat thickness, colour scores were not affected by DAR. Ingestion of LR diet increased the fasting glucose (p < 0.05) and insulin (p < 0.05) concentrations in serum. The drip loss and firmness were decreased significantly in LR vs. HR animals (p < 0.05). Densities of muscle fibre in longissimus dorsi, iliopsoas and semitendinosus were greater in LR pigs (p < 0.05). Moreover, ingestion of LR diet significantly increased myosin heavy chain (MyHC) IIa mRNA level and decreased MyHC IIb gene expression in longissimus dorsi muscle (LM) (p < 0.05). Therefore, intake of diet low in amylose/amylopectin ratio induces a better meat quality (lower drip loss and lower firmness), which could attribute to smaller myofibres, a shift to slower and/or more oxidative fibres.
Effects of vitamin E supplementation on performance, serum biochemical parameters and fatty acid composition of egg yolk in laying hens fed a diet containing ageing corn
Authors: Mu Yadong , Zhang Keying , Bai Shiping , Wang Jian Ping , Zeng Qiufeng , Ding Xuemei
Published: October 2018

This study investigated whether dietary vitamin E (VE) supplementation could alleviate any detrimental effects of ageing corn in the diet for laying hens on egg performance, egg quality, serum biochemical parameters, cholesterol content and the fatty acid (FA) profile of egg yolks. The experiment consisted of a 2 × 3 factorial design with two corn types (normal corn and ageing corn) and three concentrations of VE (0, 20 and 100 IU/kg). A total of 216 Lohmann laying hens (50‐week‐old) were randomly allocated into six treatment diets for 12 week. Each treatment had six replicates with six hens. The results showed that ageing corn significantly reduced average daily feed intake (ADFI; p < 0.01) and egg weight (p < 0.05). Dietary VE supplementation had no significant influences on egg production performance (p > 0.05). Egg yolk colour was decreased in ageing corn diets (p < 0.01), while 20 and 100 IU/kg VE significantly improved vitelline membrane strength (p < 0.01) compared with feeding of 0 IU/kg VE. Ageing corn also significantly decreased the content of cholesterol including total cholesterol (TC; p < 0.05), low density lipoprotein cholesterol (LDL‐C; p < 0.01) and very low density lipoprotein cholesterol (VLDL‐C; p < 0.05) in the serum. Feeding 100 IU/kg VE significantly increased the content of LDL‐C (p < 0.01) and VLDL‐C (p < 0.05) in the serum. Furthermore, the content of the oleic acid, docosahexaenoic acid and total monounsaturated fatty acid (MUFA) was lower (p < 0.05) and stearic acid and total saturated fatty acid (SFA) was higher (p < 0.05) in egg yolks in ageing corn diets. Ageing corn resulted in reduced feed intake, egg weights and yolk colour, but the effects of VE supplementation were independent of those of age of corn and were unable to counteract the negative effects of feeding ageing corn.
Differential Effect of Two Mental Stress Tasks on Arterial Stiffness
Authors: Matsumura Kenta , Noguchi Hiroko , Rolfe Peter , Yamakoshi Takehiro , Matsuoka Yutaka
Published: October 2018

Acute mental stress is believed to induce transient arterial dysfunction, but relatively few data are available. We therefore examined the effect of mental stress tasks that could induce differential hemodynamic responses on arterial dysfunction. Forty‐eight participants conducted either a mental arithmetic (MA) task or a mirror‐tracing (MT) task. Cardiovascular indices and arterial stiffness were measured before, during, and after these tasks. Analysis revealed that increases in arterial stiffness during the task and during recovery were more pronounced for the MA than for the MT, and that evoked hemodynamic response was more myocardial for MA than for MT. These results clearly show that MA and MT tasks that induce differential hemodynamic responses have a differential effect on arterial stiffness. This finding sheds light on the underlying mechanism that may account for the relationship between cardiovascular reactivity and cardiovascular disease.
Diversity in the section Compressa of the genus Chaetoceros (Bacillariophyceae), with description of two new species from Chinese warm waters
Authors: Xu Xiao Jing , Chen Zuo Yi , Lundholm Nina , Li Yang
Published: October 2018

Monoclonal strains of Chaetoceros species were collected from Chinese warm waters. Vegetative cells and resting spores were examined using light microscopy as well as scanning and transmission electron microscopy. Combined morphological and DNA sequence data from the hypervariable D1–D3 region of the nuclear ribosomal large subunit showed the presence of two new species within the section Compressa, herein described as Chaetoceros bifurcatus sp. nov. and C. millipedarius sp. nov. Both species possessed features typical of the section Compressa, but C. bifurcatus was characterized by the heavy intercalary setae fusing and extending together for a distance before diverging. The heavy setae were not visually contorted, lacking poroids and spines, in contrast with how the section Compressa has been defined. Chaetoceros millipedarius was characterized by a horizontal stagger of ordinary intercalary setae when the chain was seen in broad girdle view, making the chain look like a millipede. The two new species were supported by molecular phylogenetic analyses with C. bifurcatus sister to C. contortus var. ornatus, while C. millipedarius was sister to C. contortus var. contortus. Based on the morphological features exhibited in C. bifurcatus, the diagnosis of the section Compressa was emended to exclude “contorted” heavy setae and compressed valve faces.
Supporting parental caregivers of children living with life‐threatening or life‐limiting illnesses: A Delphi study
Authors: Smith Nicole R. , Bally Jill M. G. , Holtslander Lorraine , Peacock Shelley , Spurr Shelley , Hodgson‐Viden Heather , Mpofu Christopher , Zimmer Marcelline
Published: October 2018

Background

The impact of a child s life‐limiting or life‐threatening illness is significant on parents who experience a great deal of emotional, physical, and spiritual upheaval. Hope has been identified as an important inner resource for parental caregivers. Specifically, parental hope has been described as having four subproceses including Accepting Reality, Establishing Control, Restructuring Hope, and Purposive Positive Thinking. Purpose: The purpose of this Delphi study was to gather expert opinions from parents and formal care providers about the four subproceses essential to parental hope, to increase understanding of parental caregivers current support needs. As Phase one of a three‐phase study, the findings provided direction in the development of a theory‐based hope intervention.

Design and Methods

A Delphi study consisting of three rounds of survey questions and controlled feedback to experts was employed. Experts suggested strategies for each subprocess and ranked them in order of highest to lowest according to feasibility and effectiveness.

Results

Sixty‐eight experts consisting of parental caregivers of children diagnosed with life‐limiting or life‐threatening illnesses and those who care for them (community members, nurses, social workers, and physicians) were recruited to participate. Through three rounds of survey questions, response rates ranged from 92–97%. A consensus revealed eight major themes that support parental hope: Organize Basic Needs; Connect with Others; Prioritize Self‐care; Obtain Meaningful Information; Take Things Day by Day; Advocate for Parental Participation; Manifest Positivity; and Celebrate Milestones.

Practice Implications

This study identified a wide variety of psychosocial needs for parental caregivers. Results also offered direction for a theory‐based hope intervention while highlighting the need for additional research in this area. These results will provide the foundation for a booklet parents can work through in their journey of caring for a child with a life‐limiting or life‐threatening illness.
Pop-Up Property: Enacting Ownership from San Francisco to Sydney
Authors: Thorpe Amelia
Published: October 2018

Through a detailed examination of PARK(ing) Day, a loosely organized international event to reclaim street space from cars, this article reveals the intimate connection between property and its social and material context. Private claims to public streets are not uncommon. In some cases, such claims are swiftly rejected. In others, they receive recognition and respect. Focusing on the particular set of proprietary claims within PARK(ing) Day, this article examines the ways in which property on city streets is claimed and contested. Drawing primarily on fieldwork in Sydney, Australia, the analysis emphasizes the degree to which property depends on the networks in which it is situated. PARK(ing) Day was based on a creative rereading of the property producible by paying a parking meter, and this link with legality plays a key role in the event. Yet the property at issue is based on much more than that simple transaction. A more emergent and socially constructed conception of ownership is central in understanding both the making of claims to city streets on PARK(ing) Day and the range of responses they generate.
Crack as Proxy: Aggressive Federal Drug Prosecutions and the Production of Black–White Racial Inequality
Authors: Lynch Mona , Omori Marisa
Published: October 2018

In this article, we empirically examine jurisdictional variations in federal crack prosecutions to measure whether aggressive crack prosecutorial practices are associated with racial inequality in federal caseload characteristics and outcomes. Building on theories that address the production of inequality in institutional settings, we hypothesize that U.S. Attorneys’ offices that are more proactive in charging defendants with crack, relative to other kinds of drugs, and relative to case strength and seriousness, will demonstrate higher rates of black–white racial inequality in case outcomes across the entire criminal caseload. Consistent with theories of institutional racism, our findings demonstrate that aggressive crack prosecutions at the district level are a strong predictor of black–white inequality in conviction rates across the entire criminal caseload, and a much more modest predictor of inequality in final sentence outcomes. We conclude by discussing the importance of organizational-level empirical analyses for more effectively uncovering the conditions under which inequality can and does flourish in legal settings, and suggest possible future lines of inquiry along these lines.
“Legality with a Vengeance”: Reclaiming Distribution for Sociolegal Studies
Authors: Levitsky Sandra R. , Best Rachel Kahn , Garrick Jessica
Published: October 2018

The law and society community has argued for decades for an expansive understanding of what counts as “law.” But a content analysis of articles published in the Law & Society Review from its 1966 founding to the present finds that since the 1970s, the law and society community has focused its attention on laws in which the state regulates behavior, and largely ignored laws in which the state distributes resources, goods, and services. Why did socio-legal scholars avoid studying how laws determine access to such things as health, wealth, housing, education, and food? We find that socio-legal scholarship has always used “law on the books” as a starting point for analyses (often to identify departures in “law in action”) without ever offering a programmatic vision for how law might ameliorate economic inequality. As a result, when social welfare laws on the books began disappearing, socio-legal scholarship drifted away from studying law's role in creating, sustaining, and reinforcing economic inequality. We argue that socio-legal scholarship offers a wide range of analytical tools that could make important contributions to our understanding of social welfare provision.
Seeing Like an Islamic State: Shari‘a and Political Power in Sudan
Authors: Sachs Jeffrey Adam
Published: October 2018

Islamic law, or shari‘a, has been incorporated into the legal systems of many states. In much of the existing literature, this process is understood as part of the colonial and postcolonial state's attempt to render law legible—that is, codified, standardized, and abstract. In this article, I show how some state actors chose to move in the opposite direction, actively discouraging the transformation of shari‘a into a formal and codified system of law. Using the case of colonial and postcolonial Sudan, I argue that these actors viewed legal legibility as a threat to state power, recognizing the jurisgenerative potential of an informal and uncodified law.
Seasonal change in spatial variability of eelgrass epifaunal community in relation to gradients of abiotic and biotic factors
Authors: Momota Kyosuke , Nakaoka Masahiro
Published: October 2018

Seagrass‐associated macroinvertebrates (epifauna) play important roles as mediators between primary producers and higher consumers in seagrass beds. However, many aspects of the variation in the epifaunal community in seagrass beds remain to be investigated. In this study, we examined how the epifaunal community structure varied seasonally and spatially with abiotic and biotic factors in an eelgrass bed of Akkeshi, northeastern Japan. We predict that abiotic factors are more definitive of the variation in the epifaunal community than biotic factors when the eelgrass bed is less productive in early spring and late autumn, whereas biotic factors including macro‐epibiotic organisms (epiphytic macroalgae and sessile animals on eelgrass blades) are more influential when the eelgrass bed is more productive from late spring to early autumn. The epifaunal community composition varied greatly with season, and its spatial variation was correlated with different sets of abiotic and biotic factors in different seasons. Epibiotic organisms, in addition to other abiotic and biotic factors, explained some of the variation, especially in the productive summer seasons, despite the relatively low biomass of epibiotic organisms compared to that of eelgrass and epiphytic microalgae. Inconsistent with our prediction, abiotic factors were more definitive of the spatial patterns of the epifaunal communities from spring to summer when the productivity of the eelgrass bed was increasing, whereas biotic factors were found to be more important in the autumn when the productivity declined. Our result highlights the importance of epibiotic organisms on eelgrass blades to the epifaunal community, which was underappreciated in previous studies.
Mind your neighbourhood: Biotic and abiotic factors shaping the small‐scale spatial distribution of sponges (Demospongiae) in tropical urban beaches
Authors: Oliveira Franciele S. , Lanna Emilio
Published: October 2018

The distribution and abundance of a species can be determined by the interaction of that species with both the biotic and abiotic characteristics of the environment it inhabits. The Demospongiae Aplysina solangeae, Cladocroce caelum, Desmapsamma anchorata, Dysidea janiae and Tedania ignis are commonly found in urban beaches along the tropical Brazilian coast. They reproduce year round in these localities and are thus good model species candidates for studies of evolutionary developmental biology, ecotoxicology and bioprospecting. Here, we investigate how substrate and community requirements modulate the density of these species in two urban beaches in Todos os Santos Bay, Brazil, in order to better comprehend the species’ needs for settlement and growth. We assessed the density of the target species by sampling quadrats during SCUBA dives at these two beaches. Generalised additive models were used to assess how the per cent coverage of benthic organisms co‐occurring with these species influenced the density of the target species. As expected, we found that each species had different requirements for their spatial distribution, with most species being generalists. The only exception to this was found with C. caelum, which appeared to be more specialist, requiring a higher number of explanatory variables in terms of neighbouring benthos despite being the most abundant target species in both localities. A comparison of the differences observed in small‐scale localities and the regional scale is presented. Our findings on how selective these species are about their “neighbourhood” allow us to better comprehend their life histories and predict their dynamics in a changing environment.
Inbreeding tolerance as a pre‐adapted trait for invasion success in the invasive ant Brachyponera chinensis
Authors: Eyer Pierre‐André , Matsuura Kenji , Vargo Edward L. , Kobayashi Kazuya , Yashiro Toshihisa , Suehiro Wataru , Himuro Chihiro , Yokoi Tomoyuki , Guénard Benoit , Dunn Robert R. , Tsuji Kazuki
Published: October 2018

Identifying traits that facilitate species introductions and successful invasions of ecosystems represents a key issue in ecology. Following their establishment into new environments, many non‐native species exhibit phenotypic plasticity with post‐introduction changes in behaviour, morphology or life history traits that allow them to overcome the presumed loss of genetic diversity resulting in inbreeding and reduced adaptive potential. Here, we present a unique strategy in the invasive ant Brachyponera chinensis (Emery), in which inbreeding tolerance is a pre‐adapted trait for invasion success, allowing this ant to cope with genetic depletion following a genetic bottleneck. We report for the first time that inbreeding is not a consequence of the founder effect following introduction, but it is due to mating between sister queens and their brothers that pre‐exists in native populations which may have helped it circumvent the cost of invasion. We show that a genetic bottleneck does not affect the genetic diversity or the level of heterozygosity within colonies and suggest that generations of sib‐mating in native populations may have reduced inbreeding depression through purifying selection of deleterious alleles. This work highlights how a unique life history may pre‐adapt some species for biological invasions.
The obligate alkalophilic soda‐lake fungus Sodiomyces alkalinus has shifted to a protein diet
Authors: Grum‐Grzhimaylo Alexey A. , Falkoski Daniel L. , van den Heuvel Joost , Valero‐Jiménez Claudio A. , Min Byoungnam , Choi In‐Geol , Lipzen Anna , Daum Chris G. , Aanen Duur K. , Tsang Adrian , Henrissat Bernard , Bilanenko Elena N. , de Vries Ronald P. , van Kan Jan A. L. , Grigoriev Igor V. , Debets Alfons J. M.
Published: October 2018

Sodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant‐deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant‐degrading enzymes and proteinases, when compared to its closest plant‐pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall‐degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant‐based diet and has become specialized in a more protein‐rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.
Long‐term effects of superoxide and DNA repair on lizard telomeres
Authors: Olsson Mats , Friesen Christopher R. , Rollings Nicky , Sudyka Joanna , Lindsay Willow , Whittington Camilla M. , Wilson Mark
Published: October 2018

Telomeres are the non‐coding protein‐nucleotide “caps” at chromosome ends that contribute to chromosomal stability by protecting the coding parts of the linear DNA from shortening at cell division, and from erosion by reactive molecules. Recently, there has been some controversy between molecular and cell biologists, on the one hand, and evolutionary ecologists on the other, regarding whether reactive molecules erode telomeres during oxidative stress. Many studies of biochemistry and medicine have verified these relationships in cell culture, but other researchers have failed to find such effects in free‐living vertebrates. Here, we use a novel approach to measure free radicals (superoxide), mitochondrial “content” (a combined measure of mitochondrial number and size in cells), telomere length and DNA damage at two primary time points during the mating season of an annual lizard species (Ctenophorus pictus). Superoxide levels early in the mating season vary widely and elevated levels predict shorter telomeres both at that time as well as several months later. These effects are likely driven by mitochondrial content, which significantly impacts late season superoxide (cells with more mitochondria have more superoxide), but superoxide effects on telomeres are counteracted by DNA repair as revealed by 8‐hydroxy‐2′‐deoxyguanosine assays. We conclude that reactive oxygen species and DNA repair are fundamental for both short‐ and long‐term regulation of lizard telomere length with pronounced effects of early season cellular stress detectable on telomere length near lizard death.
Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions
Authors: Feng Youzhi , Chen Ruirui , Stegen James C. , Guo Zhiying , Zhang Jianwei , Li Zhongpei , Lin Xiangui
Published: October 2018

Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap, we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so, we leveraged regional‐scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM—in response to nutrient addition—influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modelling.
A synergistic role for two predicted inner membrane proteins of Escherichia coli in cell envelope integrity
Authors: Mychack Aaron , Amrutha R. N. , Chung Charlie , Cardenas Arevalo Karla , Reddy Manjula , Janakiraman Anuradha
Published: October 2018

The bacterial cytoplasmic membrane is a principal site of protein translocation, lipid and peptidoglycan biogenesis, signal transduction, transporters and energy generating components of the respiratory chain. Although 25–30% of bacterial proteomes consist of membrane proteins, a comprehensive understanding of their influence on fundamental cellular processes is incomplete. Here, we show that YciB and DcrB, two small cytoplasmic membrane proteins of previously unknown functions, play an essential synergistic role in maintaining cell envelope integrity of Escherichia coli. Lack of both YciB and DcrB results in pleiotropic cell defects including increased levels of lipopolysaccharide, membrane vesiculation, dynamic shrinking and extension of the cytoplasmic membrane accompanied by lysis and cell death. The stalling of an abundant outer membrane lipoprotein, Lpp, at the periplasmic face of the inner membrane leads to lethal inner membrane–peptidoglycan linkages. Additionally, the periplasmic chaperone Skp contributes to yciB dcrB mutant cell death by possibly mistargeting stalled porins into the inner membrane. Consistent with the idea of a compromised envelope in the yciB dcrB mutant, multiple envelope stress response systems are induced, with Cpx signal transduction being required for growth. Taken together, our results suggest a fundamental role for YciB and DcrB in cell envelope biogenesis.
Acoustic monitoring reveals the times and tides of harbor porpoise (Phocoena phocoena) distribution off central Oregon, U.S.A.
Authors: Holdman Amanda K. , Haxel Joseph H. , Klinck Holger , Torres Leigh G.
Published: October 2018

Harbor porpoises (Phocoena phocoena) are commonly observed in Oregon's nearshore marine environment yet knowledge of their ecosystem use and behavior remains limited, generating concerns for potential impacts on this species from future coastal development. Passive acoustic monitoring was used to investigate spatial and temporal variations in the presence and foraging activity of harbor porpoises off the Oregon coast from May through October 2014. Digital monitoring devices (DMONs) were deployed to record acoustic data (320 kHz sample rate) in two neighboring but bathymetrically different locations off the Oregon coast: (1) a site on the 30 m isobath in close proximity (<50 m) to a rocky reef, and (2) a site on the 60 m isobath in an open sandy environment. Data were analyzed with respect to two dynamic cyclic variables: diel and tidal phase. Porpoise presence at the rocky reef site was aligned with the ebb phase of the tidal forcing, while, harbor porpoise presence and foraging at the offshore, sandy bottom site was associated with night‐time foraging. The spatial and temporal patterns identified in this study suggest harbor porpoise habitat use is modulated by specific environmental conditions particular to each site that maximize foraging efficiency.
Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean
Authors: Leslie Matthew S. , Archer Frederick I. , Morin Phillip A.
Published: October 2018

Spinner dolphins (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because understanding population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical taxonomic levels. Results show differences between subspecies of spinner and spotted dolphins, but no support for the division of existing offshore stocks of spotted dolphins. We compare these results to previous results of genome‐wide nuclear SNP data and suggest high haplotype diversity, female dispersal, and/or relative power of the two data sets explains the differences observed. Interestingly, increasing the amount of mitochondrial data (base pairs and genes) did not increase ability to delimit population units. This study supports a genetic basis for management units at the subspecies level, and provides critical information for mitigating historical and continued fisheries impacts.
Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution
Authors: Cavender‐Bares Jeannine
Published: October 2018

ContentsSummary669I.Model clades for the study and integration of ecology and evolution670II.Oaks: an important model clade671III.Insights from the history of the American oaks for understanding community assembly and ecosystem dominance673IV.Bridging the gap between micro‐ and macroevolutionary processes relevant to ecology679V.How do we reconcile evidence for adaptive evolution with niche conservatism and long‐term stasis?682VI.High plasticity and within‐population genetic variation contribute to population persistence683VII.Emerging technologies for tracking functional change685VIII.Conclusions685Acknowledgements686References686

Ecologists and evolutionary biologists are concerned with explaining the diversity and composition of the natural world and are aware of the inextricable linkages between ecological and evolutionary processes that maintain the Earth's life support systems. Yet examination of these linkages remains challenging due to the contrasting nature of focal systems and research approaches. Model clades provide a critical means to integrate ecology and evolution, as illustrated by the oaks (genusQuercus), an important model clade, given their ecological dominance, remarkable diversity, and growing phylogenetic, genomic, and ecological data resources. Studies of the clade reveal that their history of sympatric parallel adaptive radiation continues to influence community assembly today, highlighting questions on the nature and extent of coexistence mechanisms. Flexible phenology and hydraulic traits, despite evolutionary stasis, may have enabled adaptation to a wide range of environments within and across species, contributing to their high abundance and diversity. The oaks offer fundamental insights at the intersection of ecology and evolution on the role of diversification in community assembly processes, on the importance of flexibility in key functional traits in adapting to new environments, on factors contributing to persistence of long‐lived organisms, and on evolutionary legacies that influence ecosystem function.
The extent of adaptive wild introgression in crops
Authors: Janzen Garrett M. , Wang Li , Hufford Matthew B.
Published: October 2018

The study of crop evolution has focused primarily on the process of initial domestication. Post‐domestication adaptation during the expansion of crops from their centers of origin has received considerably less attention. Recent research has revealed that, in at least some instances, crops have received introgression from their wild relatives that has facilitated adaptation to novel conditions encountered during expansion. Such adaptive introgression could have an important impact on the basic study of domestication, affecting estimates of several evolutionary processes of interest (e.g. the strength of the domestication bottleneck, the timing of domestication, the targets of selection during domestication). Identification of haplotypes introgressed from the wild may also help in the identification of alleles that are beneficial under particular environmental conditions. Here we review mounting evidence for substantial adaptive wild introgression in several crops and consider the implications of such gene flow to our understanding of crop histories.
Light regulation of coccolithophore host–virus interactions
Authors: Thamatrakoln Kimberlee , Talmy David , Haramaty Liti , Maniscalco Christopher , Latham Jason R. , Knowles Ben , Natale Frank , Coolen Marco J. L. , Follows Michael J. , Bidle Kay D.
Published: October 2018

Viruses that infect photoautotrophs have a fundamental relationship with light, given the need for host resources.

We investigated the role of light onCoccolithovirus(EhV) infection of the globally distributed coccolithophore,Emiliania huxleyi. Light was required for EhV adsorption, and viral production was highest when host cultures were maintained in continuous light or at irradiance levels of 150–300 μmol m−2 s−1. During the early stages of infection, photosynthetic electron transport remained high, while RuBisCO expression decreased concomitant with an induction of the pentose phosphate pathway, the primary source ofde novonucleotides. A mathematical model developed and fitted to the laboratory data supported the hypothesis that EhV replication was controlled by a trade‐off between host nucleotide recycling andde novosynthesis, and that photoperiod and photon flux could toggle this switch.

Laboratory results supported field observations that light was the most robust driver of EhV replication withinE. huxleyipopulations collected across a 2000 nautical mile transect in the North Atlantic.

Collectively, these findings demonstrate that light can drive host–virus interactions through a mechanistic interplay between host metabolic processes, which serve to structure infection and phytoplankton mortality in the upper ocean.
Whole‐tree nonstructural carbohydrate storage and seasonal dynamics in five temperate species
Authors: Furze Morgan E. , Huggett Brett A. , Aubrecht Donald M. , Stolz Claire D. , Carbone Mariah S. , Richardson Andrew D.
Published: October 2018

Despite the importance of nonstructural carbohydrates (NSC) for growth and survival in woody plants, we know little about whole‐treeNSCstorage. The conventional theory suggests thatNSCreserves will increase over the growing season and decrease over the dormant season. Here, we compare storage in five temperate tree species to determine the size and seasonal fluctuation of whole‐tree totalNSCpools as well as the contribution of individual organs.

NSCconcentrations in the branches, stemwood, and roots of 24 trees were measured across 12 months. We then scaled up concentrations to the whole‐tree and ecosystem levels using allometric equations and forest stand inventory data.

While whole‐tree totalNSCpools followed the conventional theory, sugar pools peaked in the dormant season and starch pools in the growing season. Seasonal depletion of totalNSCs was minimal at the whole‐tree level, but substantial at the organ level, particularly in branches. Surprisingly, roots were not the major storage organ as branches stored comparable amounts of starch throughout the year, and root reserves were not used to support springtime growth.

Scaling upNSCconcentrations to the ecosystem level, we find that commonly used, process‐based ecosystem and land surface models all overpredictNSCstorage.
Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers
Authors: Qiu Fan , Baack Eric J. , Whitney Kenneth D. , Bock Dan G. , Tetreault Hannah M. , Rieseberg Loren H. , Ungerer Mark C.
Published: October 2018

Flowering plants serve as a powerful model for studying the evolution of nuclear genome size (GS) given the tremendous GS variation that exists both within and across angiosperm lineages.

Helianthus sunflowers consist of c. 50 species native to North America that occupy diverse habitats and vary in ploidy level. In the current study, we generated a comprehensive GS database for 49 Helianthus species using flow cytometric approaches. We examined variability across the genus and present a comparative phylogenetic analysis of GS evolution in diploid Helianthus species.

Results demonstrated that different clades of diploid Helianthus species showed evolutionary patterns of GS contraction, expansion and relative stasis, with annual diploid species evolving smaller GS with the highest rate of evolution. Phylogenetic comparative analyses of diploids revealed significant negative associations of GS with temperature seasonality and cell production rate, indicating that the evolution of larger GS in Helianthus diploids may be more permissible in habitats with longer growing seasons where selection for more rapid growth may be relaxed.

The Helianthus GS database presented here and corresponding analyses of environmental and phenotypic correlates will facilitate ongoing and future research on the ultimate drivers of GS evolution in this well‐studied North American plant genus.
Arabidopsis γ‐glutamylcyclotransferase affects glutathione content and root system architecture during sulfur starvation
Authors: Joshi Naveen C. , Meyer Andreas J. , Bangash Sajid A. K. , Zheng Zhi‐Liang , Leustek Thomas
Published: October 2018

γ‐Glutamylcyclotransferase initiates glutathione degradation to component amino acids l‐glutamate, l‐cysteine and l‐glycine. The enzyme is encoded by three genes in Arabidopsis thaliana, one of which (GGCT2;1) is transcriptionally upregulated by starvation for the essential macronutrient sulfur (S). Regulation by S‐starvation suggests that GGCT2;1 mobilizes l‐cysteine from glutathione when there is insufficient sulfate for de novo l‐cysteine synthesis.

The response of wild‐type seedlings to S‐starvation was compared to ggct2;1 null mutants.

S‐starvation causes glutathione depletion in S‐starved wild‐type seedlings, but higher glutathione is maintained in the primary root tip than in other seedling tissues. Although GGCT2;1 is induced throughout seedlings, its expression is concentrated in the primary root tip where it activates the γ‐glutamyl cycle. S‐starved wild‐type plants also produce longer primary roots, and lateral root growth is suppressed. While glutathione is also rapidly depleted in ggct2;1 null seedlings, much higher glutathione is maintained in the primary root tip compared to the wild‐type. S‐starved ggct2;1 primary roots grow longer than the wild‐type, and lateral root growth is not suppressed.

These results point to a role for GGCT2;1 in S‐starvation‐response changes to root system architecture through activity of the γ‐glutamyl cycle in the primary root tip. l‐Cysteine mobilization from glutathione is not solely a function of GGCT2;1.
Beyond buzz‐pollination – departures from an adaptive plateau lead to new pollination syndromes
Authors: Dellinger Agnes S. , Chartier Marion , Fernández‐Fernández Diana , Penneys Darin S. , Alvear Marcela , Almeda Frank , Michelangeli Fabián A. , Staedler Yannick , Armbruster W. Scott , Schönenberger Jürg
Published: October 2018

Pollination syndromes describe recurring adaptation to selection imposed by distinct pollinators. We tested for pollination syndromes in Merianieae (Melastomataceae), which contain bee‐ (buzz‐), hummingbird‐, flowerpiercer‐, passerine‐, bat‐ and rodent‐pollinated species. Further, we explored trait changes correlated with the repeated shifts away from buzz‐pollination, which represents an ‘adaptive plateau’ in Melastomataceae.

We used random forest analyses to identify key traits associated with the different pollinators of 19 Merianieae species and estimated the pollination syndromes of 42 more species. We employed morphospace analyses to compare the morphological diversity (disparity) among syndromes.

We identified three pollination syndromes (‘buzz‐bee’, ‘mixed‐vertebrate’ and ‘passerine’), characterized by different pollen expulsion mechanisms and reward types, but not by traditional syndrome characters. Further, we found that ‘efficiency’ rather than ‘attraction’ traits were important for syndrome circumscription. Contrary to syndrome theory, our study supports the pooling of different pollinators (hummingbirds, bats, rodents and flowerpiercers) into the ‘mixed‐vertebrate’ syndrome, and we found that disparity was highest in the ‘buzz‐bee’ syndrome.

We conclude that the highly adaptive buzz‐pollination system may have prevented shifts towards classical pollination syndromes, but provided the starting point for the evolution of a novel set of distinct syndromes, all having retained multifunctional stamens that provide pollen expulsion, reward and attraction.
Getting closer: vein density in C4 leaves
Authors: Kumar Dhinesh , Kellogg Elizabeth A.
Published: October 2018

Contents

Summary
1260

I.
Introduction
1260

II.
Molecular and genetic mechanisms of C4 leaf venation
1262

III.
Conclusions and future perspectives
1266

Acknowledgements
1266

References
1266

C4 grasses are major contributors to the world's food supply. Their highly efficient method of carbon fixation is a unique adaptation that combines close vein spacing and distinct photosynthetic cell types. Despite its importance, the molecular genetic basis of C4 leaf development is still poorly understood. Here we summarize current knowledge of leaf venation and review recent progress in understanding molecular and genetic regulation of vascular patterning events in C4 plants. Evidence points to the interplay of auxin, brassinosteroids, SHORTROOT/SCARECROW and INDETERMINATE DOMAIN transcription factors. Identification and functional characterization of candidate regulators acting early in vascular development will be essential for further progress in understanding the precise regulation of these processes.