bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumor cell entry into the lymph node is controlled by CCL1 chemokine expressed by lymph node lymphatic sinuses
Authors: Das Suvendu , Sarrou Eliana , Podgrabinska Simona , Cassella Melanie , Mungamuri Sathish Kumar , Feirt Nikki , Gordon Ronald , Nagi Chandandeep S. , Wang Yarong , Entenberg David , Condeelis John , Skobe Mihaela
Published: July 2013

Lymphatic vessels are thought to contribute to metastasis primarily by serving as a transportation system. It is widely believed that tumor cells enter lymph nodes passively by the flow of lymph. We demonstrate that lymph node lymphatic sinuses control tumor cell entry into the lymph node, which requires active tumor cell migration. In human and mouse tissues, CCL1 protein is detected in lymph node lymphatic sinuses but not in the peripheral lymphatics. CCR8, the receptor for CCL1, is strongly expressed by human malignant melanoma. Tumor cell migration to lymphatic endothelial cells (LECs) in vitro is inhibited by blocking CCR8 or CCL1, and recombinant CCL1 promotes migration of CCR8+ tumor cells. The proinflammatory mediators TNF, IL-1β, and LPS increase CCL1 production by LECs and tumor cell migration to LECs. In a mouse model, blocking CCR8 with the soluble antagonist or knockdown with shRNA significantly decreased lymph node metastasis. Notably, inhibition of CCR8 led to the arrest of tumor cells in the collecting lymphatic vessels at the junction with the lymph node subcapsular sinus. These data identify a novel function for CCL1–CCR8 in metastasis and lymph node LECs as a critical checkpoint for the entry of metastases into the lymph nodes.
MK5 activates Rag transcription via Foxo1 in developing B cells
Authors: Chow Kwan T. , Timblin Greg A. , McWhirter Sarah M. , Schlissel Mark S.
Published: July 2013

Foxo1 is a critical, direct regulator of Rag (recombination activating gene) transcription during B cell development and is thus essential for the generation of a diverse repertoire of antigen receptors. Although Foxo1 regulation has been widely studied in many cell types, pathways regulating Foxo1 in B cells have not been fully elucidated. By screening a panel of Foxo1 mutants, we identified serine 215 on Foxo1 as a novel phosphorylation site that is essential for the activation of Rag transcription. Mutation of S215 strongly attenuated transactivation of Rag but did not affect most other Foxo1 target genes. We show that MK5, a MAPK-activated protein kinase, is a previously unidentified upstream regulator of Foxo1. MK5 was necessary and sufficient to activate Rag transcription in transformed and primary pro–B cells. Together, our experiments show that MK5 positively regulates Rag transcription via phosphorylation of Foxo1 in developing B cells.
On the use of the Cole–Cole equations in spectral induced polarization
Authors: Tarasov Andrey , Titov Konstantin
Published: July 2013

Two different equations, both of which are often called ‘the Cole–Cole equation’, are widely used to fit experimental Spectral Induced Polarization data. The data are compared on the basis of fitting model parameters: the chargeability, the time constant and the exponent. The difference between the above two equations (the Cole–Cole equation proposed by the Cole brothers and Pelton's equation) is manifested in one of the fitting parameters, the time constant. The Cole–Cole time constant is an inverse of the peak angular frequency of the imaginary conductivity, while Pelton's time constant depends on the chargeability and exponent values. The difference between the time constant values corresponding to the above two equations grows with the increase of the chargeability value, and with the decrease of the Cole–Cole exponent value. This issue must be taken into consideration when comparing the experimental data sets for high polarizability media presented in terms of the Cole–Cole parameters.
Night-time predation on post-settlement Japanese black rockfish Sebastes cheni in a macroalgal bed: effect of body length on the predation rate
Authors: Kinoshita Hikari , Kamimura Yasuhiro , Mizuno Ken-Ichiro , Shoji Jun
Published: July 2013

Recent field studies have pointed out that the vulnerability of juvenile fish to predation is higher than anticipated during night-time in vegetated habitats. Effects of abundance, body length, and growth rate on predation were examined in juvenile Japanese black rockfish in 2009–2011 in a macroalgal bed. Juvenile rockfish abundance ranged between 2.5 and 49.0 ind. 100 m–2 and the biomass of potential predators (piscivorous fish >82.5 mm) between 140.0 and 601.3 g 100 m−2. Sebastes inermis was the most dominant predator, compromising more than 50% by wet weight on all sampling days. Comparison of the total length of juveniles surviving (as original population, OP) and that of juveniles ingested (IG) by predators provided the evidence of the size-selective predation on juvenile rockfish on three of seven sampling days. The juvenile predation rate estimated as abundance of IG (N 100 m−2)/(abundance of IG + OP (N 100 m−2)) × 100100 varied between 0.4 and 12.5%. Neither juvenile rockfish abundance nor predator biomass had a significant effect on the juvenile predation rate, whereas the juvenile body length had a significant effect, smaller individuals being more vulnerable to predation. The growth-selective predation was not detected. Macroalgal habitats, although functioning as nurseries during the day, may contribute as feeding grounds for piscivorous fish predators at night leading to enhanced nocturnal predation rates.
Can behavioural ecology unite hypotheses for fish recruitment?
Authors: Jørgensen Christian , Opdal Anders Frugård , Fiksen Øyvind
Published: July 2013

Since the classical works by Hjort linked the survival of early life stages of fish to year-class strength and recruitment, fisheries science has struggled to understand the fate of fish eggs and larvae. Here we discuss how food availability will influence growth and survival of larvae when foraging behaviour is flexible and involves predation risk. We use theory to show that small larval fish with a high risk of predation should nevertheless forage intensely and maintain high growth rates. The implication of this is that food availability is more important to recruitment success than is often assumed from studies of growth rate, since the main effect of low food availability appears as increased predation rates. As larvae develop and grow bigger, they are expected to tailor their behaviour to balance food intake and predation risk, which makes it more probable that environmental fluctuations will cause growth differences. A theoretical framework including larval behaviour thus illustrates how several existing hypotheses, i.e. “bigger is better”, “stage duration”, and “growth-selective predation”, emphasize different aspects of larval success but can be understood more generally and coherently when interpreted in the light of behavioural trade-offs. This may lead to more consistent consideration of larval behaviour in biophysical models of fish recruitment.
Climate forcing and the Kuroshio/Oyashio ecosystem
Authors: Yatsu Akihiko , Chiba Sanae , Yamanaka Yasuhiro , Ito Shin-ichi , Shimizu Yugo , Kaeriyama Masahide , Watanabe Yoshioro
Published: July 2013

Yatsu, A., Chiba, S., Yamanaka, Y., Ito, S-I., Shimizu, Y., Kaeriyama, M., and Watanabe, Y. 2013. Climate forcing and the Kuroshio/Oyashio ecosystem. – ICES Journal of Marine Science, 70: 922–933. The Kuroshio and Oyashio, western boundary currents in the North Pacific, greatly influence climate, ecosystems, and fisheries in the western North Pacific and its adjacent waters. The Kuroshio/Oyashio ecosystem (KOE) shows interannual and decadal variability including regime shifts. Under a collaboration of the Climate Forcing and Marine Ecosystem Response (CFAME) Task Team and Working Group 20 (Evaluations of Climate Change Projections) of PICES, we analysed the observed time-series of physics, nutrients, chlorophyll, zooplankton abundance and phenology, and productivity, biomass, and catch of commercially important species to assess the impacts of Intergovernmental Panel on Climate Change's global change scenarios on KOE. Mechanistic linkages from climate forcing to fish population dynamics were explored for the Japanese common squid (Todarodes pacificus), Japanese sardine (Sardinops melanostictus), walleye pollock (Theragra chalcogramma), and chum salmon (Oncorhynchus keta). Future scenarios of zooplankton, commercial species, and ecosystem changes were presented based on the empirical mechanistic linkages and results of projections for physical conditions and primary production in KOE derived from both empirical knowledge and three-dimensional ecosystem-biogeochemical models. Associated data gaps, uncertainties, and implications for managers were also discussed.
Changing attitudes 1970–2012: evolution of the Norwegian management framework to prevent overfishing and to secure long-term sustainability
Authors: Gullestad Peter , Aglen Asgeir , Bjordal Åsmund , Blom Geir , Johansen Sverre , Krog Jørn , Misund Ole Arve , Røttingen Ingolf
Published: July 2013

Gullestad, P., Aglen, A., Bjordal, Å., Blom, G., Johansen, S., Krog, J., Misund, O. A., and Røttingen, I. 2014. Changing attitudes 1970–2012: evolution of the Norwegian management framework to prevent overfishing and to secure long-term sustainability. – ICES Journal of Marine Science, 71: 173–182. Fisheries have been important for livelihood in Norwegian coastal communities for centuries. The development of new fishing technology and increasing fishing capacity posed challenges for the sustainability of the fisheries. The Norwegian spring spawning herring was depleted in the1960s—with dire consequences. This event, and the subsequent efforts to rebuild the stock, was paramount to the gradual development of a coherent Norwegian policy to prevent overfishing and secure long-term sustainability. Nevertheless, overfishing continued during the ensuing transitional decades when a range of new management tools were developed and made effective. Internationally, the extension of the economic zones to 200 nautical miles, and agreement on sharing and management of joint stocks were important elements. At the national level, the development of measures to curb overcapacity, improvement of exploitation patterns through technical regulations, ban on discard and the evolution of procedures for rational decision-making for setting total allowable catches (TACs) on the basis of harvest control rules, were all decisive elements. Another crucial factor was the creation of a whole new profession of fishery inspection. We describe a system of close collaboration between specialists—scientists, fishery managers, and stakeholders—each with a distinct role in building a solid framework to prevent overfishing and secure long-term sustainability.
Data from fur seal scats reveal when Namibian Merluccius capensis are hatched and how fast they grow
Authors: Wilhelm Margit R. , Roux Jean-Paul , Moloney Coleen L. , Jarre Astrid
Published: July 2013

Wilhelm, M. R., Roux, J-P., Moloney, C. L., and Jarre, A. 2013. Data from fur seal scats reveal when Namibian Merluccius capensis are hatched and how fast they grow. – ICES Journal of Marine Science, 70: . Scat samples were collected regularly at several breeding colonies of Cape fur seals along the Namibian coast. Merluccius capensis otoliths were obtained from these samples, identified, and measured. Cohorts were easily distinguishable using otolith length measurements converted to fish total length. Growth rates of 2- to 21-month-old hake and hatch dates for each of 15 cohorts were estimated from September 1994 to October 2009 (1994–2008 cohorts) using a Schnute growth function and a non-linear mixed-effects model. The function describing growth of these young hake was length Lt (cm) at age t (years) Lt = 3.17 + (25.0 − 3.17) × [1 − e−0.665 × (t − 0.140)]/[1 − e−0.665 × (1.74–0.140)]. Cohort-specific random effects showed a population hatch date estimate of 31 July (austral winter), varying by 94 days among cohorts, from 31 May (1996 cohort) to 1 September (2004 cohort). The mean growth rate from ages 6 to 12 months was 1.26 cm month−1 for the population, ranging between 0.97 cm month−1 (1996 cohort) and 1.38 cm month−1 (2004 cohort). As this rate is almost double the previously estimated value, which is currently used in the stock assessment models, this result may have major implications for the current stock assessment results and the management of the stock. Re-examination of growth rates needs to be extended to older fish.
New insights on European hake biology and population dynamics from a sustained tagging effort in the Bay of Biscay
Authors: de Pontual Hélène , Jolivet Aurélie , Garren François , Bertignac Michel
Published: July 2013

de Pontual, H., Jolivet, A., Garren, F., and Bertignac, M. 2013. New insights on European hake biology and population dynamics from a sustained tagging effort in the Bay of Biscay. – ICES Journal of Marine Science, 70: . Following a pilot experiment that fundamentally challenged the knowledge of European hake life traits (growth and age at first maturity), a sustained tagging effort was carried out in the Bay of Biscay from 2004 to 2007. Out of 27 690 fish tagged between 2002 and 2007, 1199 (4.3%) have been recovered to date. These data have permitted a refinement of the growth parameters of the species, analysis of interannual variability, improved understanding of movements and migrations, and an examination of natural (M) and fishing mortality (F). Both L∞ and K of a von Bertalanffy growth model could be estimated using a robust non-linear regression procedure. Growth varied significantly between years, which is likely related to variation in environmental factors such as temperature. Data did not reveal seasonal movements of fish perhaps because of poor tag return rates from offshore fleets. However, results clearly revealed homing behaviour and/or inshore residency. Confounding factors hindered the estimation of mortality, which resulted in high estimates of M. The outcomes of this experiment led to substantial changes in the stock assessment conducted by ICES and call into question the findings of previous studies that have used erroneous age-based data to address topics on the ecology and dynamics of this species.
Attribution of changes in precipitation patterns in African rainforests
Authors: Otto Friederike E. L. , Jones Richard G. , Halladay Kate , Allen Myles R.
Published: July 2013

Tropical rainforests in Africa are one of the most under-researched regions in the world, but research in the Amazonian rainforest suggests potential vulnerability to climate change. Using the large ensemble of Atmosphere-only general circulation model (AGCM) simulations within the weather@home project, statistics of precipitation in the dry season of the Congo Basin rainforest are analysed. By validating the model simulation against observations, we could identify a good model performance for the June, July, August (JJA) dry season, but this result does need to be taken with caution as observed data are of poor quality. Additional validation methods have been used to investigate the applicability of probabilistic event attribution analysis from large model ensembles to a tropical region, in this case the Congo Basin. These methods corroborate the confidence in the model, leading us to believe the attribution result to be robust. That is, that there are no significant changes in the risk of low precipitation extremes during this dry season (JJA) precipitation in the Congo Basin. Results for the December, January, February dry season are less clear. The study highlights that attribution analysis has the potential to provide valuable scientific evidence of recent or anticipated climatological changes, especially in regions with sparse observational data and unclear projections of future changes. However, the strong influence of sea surface temperature teleconnection patterns on tropical precipitation provides more challenges in the set up of attribution studies than midlatitude rainfall.
Climatic and cultural changes in the west Congo Basin forests over the past 5000 years
Authors: Oslisly Richard , White Lee , Bentaleb Ilham , Favier Charly , Fontugne Michel , Gillet Jean-François , Sebag David
Published: July 2013

Central Africa includes the world's second largest rainforest block. The ecology of the region remains poorly understood, as does its vegetation and archaeological history. However, over the past 20 years, multidisciplinary scientific programmes have enhanced knowledge of old human presence and palaeoenvironments in the forestry block of Central Africa. This first regional synthesis documents significant cultural changes over the past five millennia and describes how they are linked to climate. It is now well documented that climatic conditions in the African tropics underwent significant changes throughout this period and here we demonstrate that corresponding shifts in human demography have had a strong influence on the forests. The most influential event was the decline of the strong African monsoon in the Late Holocene, resulting in serious disturbance of the forest block around 3500 BP. During the same period, populations from the north settled in the forest zone; they mastered new technologies such as pottery and fabrication of polished stone tools, and seem to have practised agriculture. The opening up of forests from 2500 BP favoured the arrival of metallurgist populations that impacted the forest. During this long period (2500–1400 BP), a remarkable increase of archaeological sites is an indication of a demographic explosion of metallurgist populations. Paradoxically, we have found evidence of pearl millet (
Pennisetum glaucum
) cultivation in the forest around 2200 BP, implying a more arid context. While Early Iron Age sites (prior to 1400 BP) and recent pre-colonial sites (two to eight centuries BP) are abundant, the period between 1600 and 1000 BP is characterized by a sharp decrease in human settlements, with a population crash between 1300 and 1000 BP over a large part of Central Africa. It is only in the eleventh century that new populations of metallurgists settled into the forest block. In this paper, we analyse the spatial and temporal distribution of 328 archaeological sites that have been reliably radiocarbon dated. The results allow us to piece together changes in the relationships between human populations and the environments in which they lived. On this basis, we discuss interactions between humans, climate and vegetation during the past five millennia and the implications of the absence of people from the landscape over three centuries. We go on to discuss modern vegetation patterns and African forest conservation in the light of these events.
Response of African humid tropical forests to recent rainfall anomalies
Authors: Asefi-Najafabady Salvi , Saatchi Sassan
Published: July 2013

During the last decade, strong negative rainfall anomalies resulting from increased sea surface temperature in the tropical Atlantic have caused extensive droughts in rainforests of western Amazonia, exerting persistent effects on the forest canopy. In contrast, there have been no significant impacts on rainforests of West and Central Africa during the same period, despite large-scale droughts and rainfall anomalies during the same period. Using a combination of rainfall observations from meteorological stations from the Climate Research Unit (CRU; 1950–2009) and satellite observations of the Tropical Rainfall Measuring Mission (TRMM; 1998–2010), we show that West and Central Africa experienced strong negative water deficit (WD) anomalies over the last decade, particularly in 2005, 2006 and 2007. These anomalies were a continuation of an increasing drying trend in the region that started in the 1970s. We monitored the response of forests to extreme rainfall anomalies of the past decade by analysing the microwave scatterometer data from QuickSCAT (1999–2009) sensitive to variations in canopy water content and structure. Unlike in Amazonia, we found no significant impacts of extreme WD events on forests of Central Africa, suggesting potential adaptability of these forests to short-term severe droughts. Only forests near the savanna boundary in West Africa and in fragmented landscapes of the northern Congo Basin responded to extreme droughts with widespread canopy disturbance that lasted only during the period of WD. Time-series analyses of CRU and TRMM data show most regions in Central and West Africa experience seasonal or decadal extreme WDs (less than −600 mm). We hypothesize that the long-term historical extreme WDs with gradual drying trends in the 1970s have increased the adaptability of humid tropical forests in Africa to droughts.
Financing and current capacity for REDD+ readiness and monitoring, measurement, reporting and verification in the Congo Basin
Authors: Maniatis Danae , Gaugris Jérôme , Mollicone Danilo , Scriven Joel , Corblin Alexis , Ndikumagenge Cleto , Aquino André , Crete Philippe , Sanz-Sanchez Maria-José
Published: July 2013

This paper provides the first critical analysis of the financing and current capacity for REDD+ readiness in the Congo Basin, with a particular focus on the REDD+ component of national forest monitoring and measurement, reporting and verification (M&MRV). We focus on three areas of analysis: (i) general financing for REDD+ readiness especially M&MRV; (ii) capacity and information for REDD+ implementation and M&MRV; (iii) prospects and challenges for REDD+ and M&MRV readiness in terms of financing and capacity. For the first area of analysis, a REDD+ and M&MRV readiness financing database was created based on the information from the REDD+ voluntary database and Internet searches. For the second area of analysis, a qualitative approach to data collection was adopted (semi-structured interviews with key stakeholders, surveys and observations). All 10 countries were visited between 2010 and 2012. We find that: (i) a significant amount of REDD+ financing flows into the Congo Basin (±US$550 million or almost half of the REDD+ financing for the African continent); (ii) across countries, there is an important disequilibrium in terms of REDD+ and M&MRV readiness financing, political engagement, comprehension and capacity, which also appears to be a key barrier to countries receiving equal resources; (iii) most financing appears to go to smaller scale (subnational) REDD+ projects; (iv) four distinct country groups in terms of REDD+ readiness and M&MRV status are identified; and (v) the Congo Basin has a distinct opportunity to have a specific REDD+ financing window for large-scale and more targeted national REDD+ programmes through a specific fund for the region.
The community resource management area mechanism: a strategy to manage African forest resources for REDD+
Authors: Asare Rebecca A. , Kyei Andrew , Mason John J.
Published: July 2013

Climate change poses a significant threat to Africa, and deforestation rates have increased in recent years. Mitigation initiatives such as REDD+ are widely considered as potentially efficient ways to generate emission reductions (or removals), conserve or sustainably manage forests, and bring benefits to communities, but effective implementation models are lacking. This paper presents the case of Ghana's Community Resource Management Area (CREMA) mechanism, an innovative natural resource governance and landscape-level planning tool that authorizes communities to manage their natural resources for economic and livelihood benefits. This paper argues that while the CREMA was originally developed to facilitate community-based wildlife management and habitat protection, it offers a promising community-based structure and process for managing African forest resources for REDD+. At a theoretical level, it conforms to the ecological, socio-cultural and economic factors that drive resource-users’ decision process and practices. And from a practical mitigation standpoint, the CREMA has the potential to help solve many of the key challenges for REDD+ in Africa, including definition of boundaries, smallholder aggregation, free prior and informed consent, ensuring permanence, preventing leakage, clarifying land tenure and carbon rights, as well as enabling equitable benefit-sharing arrangements. Ultimately, CREMA's potential as a forest management and climate change mitigation strategy that generates livelihood benefits for smallholder farmers and forest users will depend upon the willingness of African governments to support the mechanism and give it full legislative backing, and the motivation of communities to adopt the CREMA and integrate democratic decision-making and planning with their traditional values and natural resource management systems.
African tropical rainforest net carbon dioxide fluxes in the twentieth century
Authors: Fisher Joshua B. , Sikka Munish , Sitch Stephen , Ciais Philippe , Poulter Benjamin , Galbraith David , Lee Jung-Eun , Huntingford Chris , Viovy Nicolas , Zeng Ning , Ahlström Anders , Lomas Mark R. , Levy Peter E. , Frankenberg Christian , Saatchi Sassan , Malhi Yadvinder
Published: July 2013

The African humid tropical biome constitutes the second largest rainforest region, significantly impacts global carbon cycling and climate, and has undergone major changes in functioning owing to climate and land-use change over the past century. We assess changes and trends in CO
2
fluxes from 1901 to 2010 using nine land surface models forced with common driving data, and depict the inter-model variability as the uncertainty in fluxes. The biome is estimated to be a natural (no disturbance) net carbon sink (−0.02 kg C m
−2
yr
−1
or −0.04 Pg C yr
−1
,
p
< 0.05) with increasing strength fourfold in the second half of the century. The models were in close agreement on net CO
2
flux at the beginning of the century (
σ
1901
= 0.02 kg C m
−2
yr
−1
), but diverged exponentially throughout the century (
σ
2010
= 0.03 kg C m
−2
yr
−1
). The increasing uncertainty is due to differences in sensitivity to increasing atmospheric CO
2
, but not increasing water stress, despite a decrease in precipitation and increase in air temperature. However, the largest uncertainties were associated with the most extreme drought events of the century. These results highlight the need to constrain modelled CO
2
fluxes with increasing atmospheric CO
2
concentrations and extreme climatic events, as the uncertainties will only amplify in the next century.
The national determinants of deforestation in sub-Saharan Africa
Authors: Rudel Thomas K.
Published: July 2013

For decades, the dynamics of tropical deforestation in sub-Saharan Africa (SSA) have defied easy explanation. The rates of deforestation have been lower than elsewhere in the tropics, and the driving forces evident in other places, government new land settlement schemes and industrialized agriculture, have largely been absent in SSA. The context and causes for African deforestation become clearer through an analysis of new, national-level data on forest cover change for SSA countries for the 2000–2005 period. The recent dynamic in SSA varies from dry to wet biomes. Deforestation occurred at faster rates in nations with predominantly dry forests. The wetter Congo basin countries had lower rates of deforestation, in part because tax receipts from oil and mineral industries in this region spurred rural to urban migration, declines in agriculture and increased imports of cereals from abroad. In this respect, the Congo basin countries may be experiencing an oil and mineral fuelled forest transition. Small farmers play a more important role in African deforestation than they do in southeast Asia and Latin America, in part because small-scale agriculture remains one of the few livelihoods open to rural peoples.
Determining the response of African biota to climate change: using the past to model the future
Authors: Willis K. J. , Bennett K. D. , Burrough S. L. , Macias-Fauria M. , Tovar C.
Published: July 2013

Prediction of biotic responses to future climate change in tropical Africa tends to be based on two modelling approaches: bioclimatic species envelope models and dynamic vegetation models. Another complementary but underused approach is to examine biotic responses to similar climatic changes in the past as evidenced in fossil and historical records. This paper reviews these records and highlights the information that they provide in terms of understanding the local- and regional-scale responses of African vegetation to future climate change. A key point that emerges is that a move to warmer and wetter conditions in the past resulted in a large increase in biomass and a range distribution of woody plants up to 400–500 km north of its present location, the so-called greening of the Sahara. By contrast, a transition to warmer and drier conditions resulted in a reduction in woody vegetation in many regions and an increase in grass/savanna-dominated landscapes. The rapid rate of climate warming coming into the current interglacial resulted in a dramatic increase in community turnover, but there is little evidence for widespread extinctions. However, huge variation in biotic response in both space and time is apparent with, in some cases, totally different responses to the same climatic driver. This highlights the importance of local features such as soils, topography and also internal biotic factors in determining responses and resilience of the African biota to climate change, information that is difficult to obtain from modelling but is abundant in palaeoecological records.
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
Authors: Omasits Ulrich , Quebatte Maxime , Stekhoven Daniel J. , Fortes Claudia , Roschitzki Bernd , Robinson Mark D. , Dehio Christoph , Ahrens Christian H.
Published: July 2013

Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction ofBartonella henselaewith its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ∼90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.
Honey bee protein atlas at organ-level resolution
Authors: Chan Queenie W.T. , Chan Man Yi , Logan Michelle , Fang Yuan , Higo Heather , Foster Leonard J.
Published: July 2013

Genome sequencing has provided us with gene lists but cannot tell us where and how their encoded products work together to support life. Complex organisms rely on differential expression of subsets of genes/proteins in organs and tissues, and, in concert, evolved to their present state as they function together to improve an organism's overall reproductive fitness. Proteomics studies of individual organs help us understand their basic functions, but this reductionist approach misses the larger context of the whole organism. This problem could be circumvented if all the organs in an organism were comprehensively studied by the same methodology and analyzed together. Using honey bees (Apis mellifera L.) as a model system, we report here an initial whole proteome of a complex organism, measuring 29 different organ/tissue types among the three honey bee castes: queen, drone, and worker. The data reveal that, e.g., workers have a heightened capacity to deal with environmental toxins and queens have a far more robust pheromone detection system than their nestmates. The data also suggest that workers altruistically sacrifice not only their own reproductive capacity but also their immune potential in favor of their queen. Finally, organ-level resolution of protein expression offers a systematic insight into how organs may have developed.
Description of a new species of Orphinus Motschulsky 1858 (Coleoptera: Dermestidae: Megatominae), with a key and checklist of known species from Papua New Guinea
Authors: Kadej Marcin , Háva Jiří
Published: July 2013

Orphinus missae, sp. nov., is described from Papua New Giunea. The habitus, antenna and genitalia are illustrated and compared with related species. A key to the known dermestid species from Papua New Guinea is presented. A revised checklist for species of the family Dermestidae from Irian Jaya and Papua New Guinea is also provided.
Morphological versus molecular identification of Culex annulirostris Skuse and Culex palpalis Taylor: key members of the Culex sitiens (Diptera: Culicidae) subgroup in Australasia
Authors: Jansen Cassie C , Hemmerter Stéphane , van den Hurk Andrew F , Whelan Peter I , Beebe Nigel W
Published: July 2013

Members of the Culex sitiens subgroup of mosquitoes are important arbovirus vectors in the Australasian region. However, some species in this group, particularly Cx. annulirostris and Cx. palpalis, are difficult to distinguish based on morphological characters alone. We evaluated the reliability of morphological characters commonly used in taxonomic keys against a PCR‐based diagnostic tool that examined the ribosomal ITS1 gene region. Although reliable morphological characters allow identification, molecular identification remains the most accurate means for distinguishing Cx. annulirostris and Cx. palpalis.
In Vitro Comparison of the Delivery of Gaseous Microemboli and Hemodynamic Energy for a Diagonal and a Roller Pump During Simulated Infantile Cardiopulmonary Bypass Procedures
Authors: Dhami Ranjodh , Wang Shigang , Kunselman Allen R. , Ündar Akif
Published: July 2013

Cardiopulmonary bypass (CPB) is used for a variety of procedures in pediatric patients. Flow settings of the CPB pump have dramatic effects on patient outcome, and gaseous microemboli delivery within the CPB circuit has been linked to neurological complications. To ensure the ongoing improvement of pediatric CPB, consistent evaluation and improvement of the equipment is necessary. In this study we analyze the Jostra HL‐20 roller pump (Jostra USA, Austin, TX, USA) and a Medos Deltastream DP3 diagonal pump (MEDOS Medizintechnik AG, Stolberg, Germany) which has not yet received Food and Drug Administration approval. An infant CPB model with heparinized human blood is used to quantify the gaseous microemboli delivery (via an Emboli Detection and Classification Quantifier), as well as the hemodynamic energy delivered under flow rates of 400, 800, and 1200 mL/min. Results show that at most flow settings the DP3 delivers fewer microemboli than the Jostra roller pump at the pre‐oxygenator site, with an exception at 1200 mL/min under pulsatile mode. The total volume and the number of gaseous microemboli greater than 40 μm in diameter were lower in the DP3 group. The HL‐20 exhibits less stolen blood flow (except at 1200 mL/min) and oxygenator pressure drops in both pulsatile and nonpulsatile mode. Additionally, under pulsatile flow the DP3 delivers greater surplus hemodynamic energy. Both pumps produce relatively few microemboli and deliver adequate hemodynamic energy to the pseudo‐patient, with the DP3 performing slightly better under most flow settings.
Anti‐Inflammatory Strategies to Reduce Acute Kidney Injury in Cardiac Surgery Patients: A Meta‐Analysis of Randomized Controlled Trials
Authors: Scrascia Giuseppe , Guida Pietro , Rotunno Crescenzia , de Luca Tupputi Schinosa Luigi , Paparella Domenico
Published: July 2013

Acute kidney injury (AKI) after cardiac operations is a serious complication associated with postoperative mortality. Multiple factors contribute to AKI development, principally ischemia‐reperfusion injury and inflammatory response. It is well proven that glucocorticoid administration, leukocyte filter application, and miniaturized extracorporeal circuits (MECC) modulate inflammatory response. We conducted a systematic review of randomized controlled trials (RCTs) in which one of these inflammatory system modulation strategies was used, with the aim to evaluate the effects on postoperative AKI. MEDLINE and Cochrane Library were screened through November 2011 for RCTs in which an inflammatory system modulation strategy was adopted. Included were trials that reported data about postoperative renal outcomes. Because AKI was defined by different criteria, including biochemical determinations, urine output, or dialysis requirement, we unified renal outcome as worsening renal function (WRF). We identified 14 trials for steroids administration (931 patients, WRF incidence [treatment vs. placebo]: 2.7% vs. 2.4%; OR: 1.13; 95% CI: 0.53–2.43; P = 0.79), 9 trials for MECC (947 patients, WRF incidence: 2.4% vs. 0.9%; OR: 0.47; 95% CI: 0.18–1.25; P = 0.13), 6 trials for leukocyte filters (374 patients, WRF incidence: 1.1% vs. 7.5%; OR: 0.18; 95% CI: 0.05–0.64; P = 0.008). Only leukocyte filters effectively reduced WRF incidence. Not all cardiopulmonary bypass‐related anti‐inflammatory strategies analyzed reduced renal damage after cardiac operations. In adult patients, probably other factors are predominant on inflammation in determining AKI, and only leukocyte filters were effective. Large multicenter RCTs are needed in order to better evaluate the role of inflammation in AKI development after cardiac operations.
Spacing access to justice: geographical perspectives on disabled people's interactions with the criminal justice system as victims of crime
Authors: Edwards Claire
Published: July 2013

Over the past two decades, research emerging from the sub‐discipline of ‘geographies of disability’ has highlighted the significant socio‐spatial barriers that shape disabled people's everyday lives. Disabled people's battles to obtain equitable access through the justice system when they are victims of crime is one such arena in which these barriers become readily apparent, and yet to date, geographers' engagement with the spaces of the criminal justice system has been noticeably absent. This paper seeks to redress this lacuna by discussing the findings of qualitative research undertaken in Ireland on disabled people's experiences of the criminal justice system as victims of crime. It highlights not just how the justice system presents practical barriers to disabled people such as inaccessible courthouses or Garda stations, but also the fundamental ways in which legislation constitutes certain groups of disabled people as vulnerable or incapable, and therefore ‘out‐of‐place’ in the justice system. The paper makes a case for building disciplinary connections between geographies of disability, geographies of crime and ‘critical legal geographies’ in rendering these barriers visible.
Impact of autogenous concentrated bone marrow aspirate on bone regeneration after sinus floor augmentation with a bovine bone substitute – a split‐mouth pilot study
Authors: Wildburger Angelika , Payer Michael , Jakse Norbert , Strunk Dirk , Etchard‐Liechtenstein Nathalie , Sauerbier Sebastian
Published: July 2013

Purpose

Mesenchymal stem cells (MSC) with biomaterials have osteoinductive potential. The aim of this study was to evaluate early bone formation in xenogenic sinus grafts in a direct comparison with and without MSCs after 3 and 6 months. Literature on bone formation in pure xenogenic graft materials after 3 months in a human model is still lacking.

Materials and methods

In a split‐mouth design, seven patients with a bilateral highly atrophic posterior maxilla were included. The test side was grafted with MSCs from concentrated bone marrow aspirate admixed to the bone graft material. On the control side, pure bovine bone material was applied. Biopsies were taken navigated after 3 and 6 months.

Results

After 3 months, new bone formation in the control group was 11.8% (SD 6.2%) and in the test group 7.4% (SD 4.1%). After 6 months, the control group showed 13.9% (SD 8.5%) of new bone and the test group 13.5% NB (SD 5.4%). The fraction of bovine bone material after 3 months was 42.6% (SD 3.5%) in the test group and 34.9% (SD 11.8%) in the control group. After 6 months, the biomaterial content was comparable at both sides (test 36.2%, SD 7.8%; control 39.5%, SD 9.3%).

Conclusions

There was no significant difference in new bone formation between the test and control group with n = 7. The results may be dominated by the high mineral content of the biomaterial but could nevertheless be valuable for meta‐analysis in the future.
Quetiapine Fumarate for the Treatment of Multiple Sclerosis: Focus on Myelin Repair
Authors: Zhornitsky Simon , Wee Yong Voon , Koch Marcus W. , Mackie Aaron , Potvin Stéphane , Patten Scott B. , Metz Luanne M.
Published: July 2013

Multiple sclerosis (MS) is a central nervous system disorder that is associated with progressive oligodendrocyte and neuronal loss, axonal degeneration, and demyelination. Several medications that mitigate immune abnormalities reduce both the frequency of relapses and inflammation on magnetic resonance imaging, leading to improved outcomes for people with the relapsing–remitting form of MS. However, there are no treatments for the progressive forms of MS where neurons and axons continue to degenerate; here, neuroprotective therapies, or medications that rebuild myelin to confer axonal well‐being, may be useful. Quetiapine fumarate is an atypical antipsychotic with reported remyelinating and neuroprotective properties in inflammatory and noninflammatory models of demyelination, including experimental autoimmune encephalomyelitis, and both cuprizone‐ and global cerebral ischemia‐induced demyelination. Preclinical studies suggest that quetiapine may exert these effects by stimulating proliferation and maturation of oligodendrocytes, releasing neurotrophic factors, increasing antioxidant defences, scavenging for free radicals, and inhibiting activated microglia, astrocytes, and T lymphocytes. Additionally, quetiapine may be beneficial for psychiatric and nonpsychiatric symptoms of MS including depression, anxiety, insomnia, and possibly even pain. These data indicate that clinical trials are justified to determine the safety, tolerability, and efficacy of quetiapine fumarate in MS.
Effects of Growth Form and Functional Traits on Response of Woody Plants to Clearing and Fragmentation of Subtropical Rainforest
Authors: KOOYMAN R. M. , ZANNE A. E. , GALLAGHER R. V. , CORNWELL W. , ROSSETTO M. , O'CONNOR P. , PARKES E. A. , CATTERALL C. F. , LAFFAN S. W. , LUSK C. H.
Published: July 2013

The conservation implications of large‐scale rainforest clearing and fragmentation on the persistence of functional and taxonomic diversity remain poorly understood. If traits represent adaptive strategies of plant species to particular circumstances, the expectation is that the effect of forest clearing and fragmentation will be affected by species functional traits, particularly those related to dispersal. We used species occurrence data for woody plants in 46 rainforest patches across 75,000 ha largely cleared of forest by the early 1900s to determine the combined effects of area reduction, fragmentation, and patch size on the taxonomic structure and functional diversity of subtropical rainforest. We compiled species trait values for leaf area, seed dry mass, wood density, and maximum height and calculated species niche breadths. Taxonomic structure, trait values (means, ranges), and the functional diversity of assemblages of climbing and free‐standing plants in remnant patches were quantified. Larger rainforest patches had higher species richness. Species in smaller patches were taxonomically less related than species in larger patches. Free‐standing plants had a high percentage of frugivore dispersed seeds; climbers had a high proportion of small wind‐dispersed seeds. Connections between the patchy spatial distribution of free‐standing species, larger seed sizes, and dispersal syndrome were weak. Assemblages of free‐standing plants in patches showed more taxonomic and spatial structuring than climbing plants. Smaller isolated patches retained relatively high functional diversity and similar taxonomic structure to larger tracts of forest despite lower species richness. The response of woody plants to clearing and fragmentation of subtropical rainforest differed between climbers and slow‐growing mature‐phase forest trees but not between climbers and pioneer trees. Quantifying taxonomic structure and functional diversity provides an improved basis for conservation planning and management by elucidating the effects of forest‐area reduction and fragmentation.

Efectos de la Forma de Crecimiento y Atributos Funcionales en la Respuesta de Plantas Leñosas al Desmonte y Fragmentación de Bosque Lluvioso Subtropical
Practical Recommendations to Help Students Bridge the Research–Implementation Gap and Promote Conservation
Authors: PIETRI DIANA M. , GURNEY GEORGINA G. , BENITEZ‐VINA NANCY , KUKLOK AUDREY , MAXWELL SARA M. , WHITING LIBBY , VINA MICHAEL A. , JENKINS LEKELIA D.
Published: July 2013

Seasoned conservation researchers often struggle to bridge the research–implementation gap and promote the translation of their work into meaningful conservation actions. Graduate students face the same problems and must contend with obstacles such as limited opportunities for relevant interdisciplinary training and a lack of institutional support for application of research results. However, students also have a crucial set of opportunities (e.g., access to academic resources outside their degree programs and opportunities to design research projects promoting collaboration with stakeholders) at their disposal to address these problems. On the basis of results of breakout discussions at a symposium on the human dimensions of the ocean, a review of the literature, and our own experiences, we devised recommendations on how graduate students can create resources within their academic institutions, institutionalize resources, and engage with stakeholders to promote real‐world conservation outcomes. Within their academic institutions, graduate students should foster links to practitioners and promote knowledge and skill sharing among students. To institutionalize resources, students should cultivate student leaders and faculty sponsors, systematically document their program activities, and engage in strategic planning to promote the sustainability of their efforts. While conducting research, students should create connections to and engage actively with stakeholders in their relevant study areas and disseminate research results both to stakeholders and the broader public. Our recommendations can serve as a template for graduate students wishing to bridge the research–implementation gap, both during their current studies and in their future careers as conservation researchers and practitioners.

Recomendaciones Prácticas para Ayudar a Estudiantes a Vencer la Brecha entre Investigación e Implementación y Promover la Conservación