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Kidney transplantation is the best treatment option for patients with end-stage renal disease owing to improved survival and quality of life compared with dialysis. The surgical approach to kidney transplantation has been somewhat stagnant in the past 50 years, with the open approach being the only available option. In this scenario, evidence of reduced surgery-related morbidity after the introduction of robotics into several surgical fields has induced surgeons to consider robot-assisted kidney transplantation (RAKT) as an alternative approach to these fragile and immunocompromised patients. Since 2014, when the RAKT technique was standardized thanks to the pioneering collaboration between the Vattikuti Urology Institute and the Medanta hospital (Vattikuti Urology Institute-Medanta), several centres worldwide implemented RAKT programmes, providing interesting results regarding the safety and feasibility of this procedure. However, RAKT is still considered an alternative procedure to be offered mainly in the living donor setting, owing to various possible drawbacks such as prolonged rewarming time, demanding learning curve, and difficulties in carrying out this procedure in challenging scenarios (such as patients with obesity, severe atherosclerosis of the iliac vessels, deceased donor setting, or paediatric recipients). Nevertheless, the refinement of robotic platforms through the implementation of novel technologies as well as the encouraging results from multicentre collaborations under the umbrella of the European Association of Urology Robotic Urology Section are currently expanding the boundaries of RAKT, making this surgical procedure a real alternative to the open approach., (© 2024. Springer Nature Limited.)

Early vocabulary development is crucial for future cognitive and academic outcomes, and parent-child booksharing has been recognized as a powerful home literacy practice to promote word learning. However, evidence about the link between booksharing and language development in diverse cultural and socioeconomic settings is currently limited, hindering the formulation of a broadly applicable framework to understand the favorable conditions for early vocabulary development. This study explores the relationship between booksharing and early receptive and expressive vocabulary in a sample of 183 mothers and their toddlers in Costa Rica, a context where reading is not a common practice and children have limited access to books. Mothers completed an interview about their booksharing practices and reported children's receptive and expressive vocabulary. Results demonstrated a positive link between maternal booksharing and children's expressive vocabulary. Child gender moderated the link between booksharing and receptive vocabulary, exhibiting a stronger association in girls than in boys. Mothers with lower education levels reported higher expressive vocabulary scores for their children than mothers with higher education levels. These findings underscore the significance of booksharing in the home literacy environment, even in cultural contexts with distinct reading practices. Moreover, they highlight the need to incorporate sociocultural factors into comprehensive accounts concerning the role of booksharing in early word learning., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Karate athletes strategically use lower-limb techniques in combat, with the roundhouse kick ( mawashi geri ) being highly effective in kumite. To quickly improve the technical performance before training or competitions, conditioning activities (CAs) are often utilized. Recently, Whole-Body Vibration (WBV) has emerged as a potential conditioning activity (CA). This study aimed to analyze the acute effects of WBV as a CA on the performance of the mawashi geri . The sample included sixteen male karate athletes. The study had a familiarization and two experimental sessions: one with WBV and the other without (NWBV), conducted randomly and counterbalanced, each preceded and followed by a mawashi geri assessment on a force platform. During the CA intervention, the participants performed four sets of isometric half-squats on a vibration platform at a frequency of 26 Hz and an amplitude of 4 mm in the WBV condition, while the platform was off in the NWBV condition. A significant reduction in the mawashi geri attack phase time was observed under the WBV condition [pre: 0.31 ± 0.03 s; post: 0.30 ± 0.03 s] compared to the NWBV condition [pre: 0.31 ± 0.04 s; post: 0.32 ± 0.03 s] ( p = 0.02). However, no differences were noted regarding the impact force or other kinetic variables between the conditions. Therefore, WBV did not increase the performance of the kinetic and kinematic variables of the mawashi geri in karate athletes, but it is possible that there is a positive effect on attack time, suggesting that further studies with different vibration protocol configurations would be beneficial.

Evidence-based instructional practices (EBIPs) have been shown to benefit students in undergraduate biology, but little is known about the degree to which community college (CC) biology instructors use EBIPs or the barriers they encounter. We surveyed CC biology instructors to characterize how they use EBIPs, their capacity to use EBIPs, and perceived barriers to their use, and to explore which factors are associated with EBIP use. CC biology instructors report using EBIPs to a similar degree as other populations of undergraduate biology faculty; they generally believe EBIPs to be effective and are motivated to use EBIPs. Consistent with the theory of planned behavior, instructor belief in EBIP effectiveness, collegial support, and perceived knowledge of and skill in using EBIPs positively influence their use. The main barriers to using EBIPs reported by CC instructors included the need to cover large amounts of course content, lack of time to prepare for using EBIPs, and student resistance. Our findings point to a number of approaches that may promote the use of EBIPs by CC biology instructors, including professional development to increase instructor knowledge and skill, addressing tensions between content volume and the use of EBIPs, and providing resources to make implementing EBIPs time efficient., Competing Interests: Conflicts of Interest: The authors declare no conflicts of interest.

Advanced glycation end products (AGEs) are a diverse group of compounds that are formed as a result of the non-enzymatic reaction between a reducing sugar such as glucose and the free NH2 groups of an amino acid in a protein or other biomolecule. The chemical reaction, by which these products are generated, is known as the Maillard reaction and occurs as a part of the body's normal metabolism. Such a reaction is enhanced during diabetes due to hyperglycemia, but it can also occur during the preparation, processing, and preservation of certain foods. Therefore, AGEs can also be obtained from the diet (d-AGE) and contribute to an increase of the total serum pool of these compounds. They have been implicated in a wide variety of pathological processes, mainly because of their ability to induce inflammatory responses and oxidative stress increase. They are extensively accumulated as a part of the normal aging, especially in tissues rich in long half-life proteins, which can compromise the physiology of these tissues. d-AGEs are abundant in diets rich in processed fats and sugars. This review is addressed to the current knowledge on these products and their impact on the immunomodulation of various mechanisms that may contribute to exacerbation of the diabetes pathophysiology., (© 2024 Adriana Pedreanez et al., published by Sciendo.)

Background: The optimal oncologic surveillance in patients with upper tract urothelial carcinoma (UTUC) elected for conservative treatment is still a matter of debate., Methods: Patients elected for endoscopic treatment of UTUC were followed up according to EAU guidelines recommendations after treatment. Bladder cancer recurrence-free survival (BCa-RFS), UTUC recurrence-free survival (UTUC-RFS), radical nephroureterectomy-free survival (RNU-FS), and cancer-specific survival (CSS) were estimated using the Kaplan-Meier method. The crude risks of BCa and UTUC recurrences over time were estimated with the Locally Weighted Scatterplot Smoothing method., Results: Overall, 54 and 55 patients had low- and high-risk diseases, respectively. Median follow-up was 46.9 (IQR: 28.7-68.7) and 36.9 (IQR: 19.8-60.1) months in low and high-risk patients, respectively. In low-risk patients, BCa recurrence risk was more than 20% at 24 months follow-up. At 60 months, time point after which cystoscopy and imaging should be interrupted, the risk of BCa recurrence and UTUC recurrence were 14% and 7%, respectively. In high-risk patients, the risk of BCa and UTUC recurrence at 36 months was approximately 40% and 10%, respectively. Conversely, at 60 months, the risk of bladder recurrence and UTUC recurrence was 28% and 8%, respectively., Conclusions: For low-risk patients, cystoscopy should be performed semi-annually until 24 months, while upper tract assessment should be obtained up to 60 months, as per current EAU guidelines recommendations. For high-risk patients, upper tract assessment should be intensified to semi-annually up to 36 months, then obtained yearly. Conversely, cystoscopy should be ideally performed semi-annually until 60 months and yearly thereafter.

Objectives: To identify the predictive factors of prostate cancer extracapsular extension (ECE) in an institutional cohort of patients who underwent multiparametric MRI of the prostate prior to radical prostatectomy (RP)., Patients and Methods: Overall, 126 patients met the selection criteria, and their medical records were retrospectively collected and analysed; 2 experienced radiologists reviewed the imaging studies. Logistic regression analysis was conducted to identify the variables associated to ECE at whole-mount histology of RP specimens; according to the statistically significant variables associated, a predictive model was developed and calibrated with the Hosmer-Lomeshow test., Results: The predictive ability to detect ECE with the generated model was 81.4% by including the length of capsular involvement (LCI) and intraprostatic perineural invasion (IPNI). The predictive accuracy of the model at the ROC curve analysis showed an area under the curve (AUC) of 0.83 [95% CI (0.76-0.90)], p < 0.001. Concordance between radiologists was substantial in all parameters examined (p < 0.001). Limitations include the retrospective design, limited number of cases, and MRI images reassessment according to PI-RADS v2.0., Conclusion: The LCI is the most robust MRI factor associated to ECE; in our series, we found a strong predictive accuracy when combined in a model with the IPNI presence. This outcome may prompt a change in the definition of PI-RADS score 5., (© 2024. The Author(s).)

Introduction: Inguinal lymph node dissection (ILND) plays an important role for both staging and treatment purposes in patients diagnosed with penile carcinoma (PeCa). Video-endoscopic inguinal lymphadenectomy (VEIL) has been introduced to reduce complications, and in those patients elected for bilateral ILND, a simultaneous bilateral VEIL (sB-VEIL) has also been proposed. This study aimed to investigate the feasibility, safety, and preliminary oncological outcomes of sB-VEIL compared to consecutive bilateral VEIL (cB-VEIL)., Material and Methods: Clinical N0-2 patients diagnosed with PeCa and treated with cB-VEIL and sB-VEIL between 2015 and 2023 at our institution were included. Modified ILND was performed in cN0 patients, while cN+ patients underwent a radical approach. Intra- and postoperative complications, operative time, time of drainage maintenance, length of hospital stay and readmission within 90 days, as well as lymph node yield, were compared between the two groups., Results: Overall, 30 patients were submitted to B-VEIL. Of these, 20 and 10 patients underwent cB-VEIL and sB-VEIL, respectively. Overall, 16 (80%) and 7 (70%) patients were submitted to radical ILND due to cN1-2 disease in the cB-VEIL and sB-VEIL groups, respectively. No statistically significant difference emerged in terms of median nodal yield (13.5 vs. 14, p = 0.7) and median positive LNs ( p = 0.9). sD-VEIL was associated with a shorter operative time (170 vs. 240 min, p < 0.01). No statistically significant difference emerged in terms of intraoperative estimated blood loss, length of hospital stay, time to drainage tube removal, major complications, and hospital readmission in the cB-VEIL and sB-VEIL groups, respectively (all p > 0.05)., Conclusions: Simultaneous bilateral VEIL is a feasible and safe technique in patients with PeCA, showing similar oncological results and shorter operative time compared to a consecutive bilateral approach. Patients with higher preoperative comorbidity burden or anesthesiological risk are those who may benefit the most from this technique.

Purpose: To provide a new model to predict long-term renal function impairment after partial nephrectomy (PN)., Methods: Data of consecutive patients who underwent minimally invasive PN from 2005 to 2022 were analyzed. A minimum of 12 months of follow-up was required. We relied on a machine-learning algorithm, namely classification and regression tree (CART), to identify the predictors and associated clusters of chronic kidney disease (CKD) stage migration during follow-up., Results: 568 patients underwent minimally invasive PN at our center. A total of 381 patients met our inclusion criteria. The median follow-up was 69 (IQR 38-99) months. A total of 103 (27%) patients experienced CKD stage migration at last follow-up. Progression of CKD stage after surgery, ACCI and baseline CKD stage were selected as the most informative risk factors to predict CKD progression, leading to the creation of four clusters. The progression of CKD stage rates for cluster #1 (no progression of CKD stage after surgery, baseline CKD stage 1-2, ACCI 1-4), #2 (no progression of CKD stage after surgery, baseline CKD stage 1-2, ACCI ≥ 5), #3 (no progression of CKD stage after surgery and baseline CKD stage 3-4-5) and #4 (progression of CKD stage after surgery) were 6.9%, 28.2%, 37.1%, and 69.6%, respectively. The c-index of the model was 0.75., Conclusion: We developed a new model to predict long-term renal function impairment after PN where the perioperative loss of renal function plays a pivotal role to predict lack of functional recovery. This model could help identify patients in whom functional follow-up should be intensified to minimize possible worsening factors of renal function., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Nowadays, there is no standard non-surgical treatment for patients with nonmuscle invasive bladder cancer (NMIBC) in whom Bacillus Calmette-Güerin (BCG) therapy has failed., Objectives: To assess the clinical and oncological outcomes of sequential treatment with Bacillus Calmette-Guerin (BCG) and Mitomycin C (MMC) administered with Electromotive Drug Administration (EMDA) in patients with high-risk NMIBC who fail BCG immunotherapy., Material and Methods: We retrospectively studied patients with NMIBC who failed BCG and received alternating BCG and Mitomycin C with EMDA between 2010 and 2020. Treatment schedule consisted in an induction therapy with 6 instillations (BCG, BCG, MMC + EMDA, BCG, BCG, MMC + EMDA) and a 1-year maintenance. Complete response (CR) was defined as the absence of high-grade (HG) recurrences during follow-up, and progression was defined as the occurrence of muscle invasive or metastatic disease. CR rate was estimated at 3, 6, 12, and 24 months. Progression rate and toxicity were also assessed., Results: Twenty-two patients were included with a median age of 73 years. Fifty percent of tumors were single, 90% were smaller than 1.5cm, 40% were GII (HG) and 40% were Ta. CR rate was 95.5%, 81% and 70% at 3 and 6 months, 12 months and 24 months, respectively. With a median follow-up of 28.8 months, 6 patients (27%) presented HG recurrence and only 1 patient (4.5%) progressed and ended in cystectomy. This patient died due to metastatic disease. Treatment was well tolerated and 22% of the patients presented adverse effects, being dysuria the most frequent one., Conclusion: Sequential treatment with BCG and Mitomycin C with EMDA achieved good responses and low toxicity in selected patients who did not respond to BCG. Only 1 patient ended in cystectomy and died due to metastatic disease, therefore, cystectomy was avoided in most cases., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Cardiovascular complications are the main cause of mortality and morbidity in the diabetic patients, in whom changes in myocardial structure and function have been described. Numerous molecular mechanisms have been proposed that could contribute to the development of a cardiac damage. In this regard, angiotensin II (Ang II), a proinflammatory peptide that constitutes the main effector of the renin-angiotensin system (RAS) has taken a relevant role. The aim of this review was to analyze the role of Ang II in the different biochemical pathways that could be involved in the development of cardiovascular damage during diabetes. We performed an exhaustive review in the main databases, using the following terms: angiotensin II, cardiovascular damage, renin angiotensin system, inflammation, and diabetes mellitus. Classically, the RAS has been defined as a complex system of enzymes, receptors, and peptides that help control the blood pressure and the fluid homeostasis. However, in recent years, this concept has undergone substantial changes. Although this system has been known for decades, recent discoveries in cellular and molecular biology, as well as cardiovascular physiology, have introduced a better understanding of its function and relationship to the development of the diabetic cardiomyopathy., (© 2022 Adriana Pedreanez et al., published by Sciendo.)

Camelids (camels, dromedaries, alpacas, llamas, and vicuñas) contain in their serum conventional heterodimeric antibodies as well as antibodies with no light chains (L) in their structure and composed of only heavy chains (H), called as HcAbs (heavy chain antibodies). Variable fragments derived from these antibodies, called as VHH or nanoantibodies (Nbs), have also been described. Since their discovery, Nbs have been widely used in the fields of research, diagnostics, and pharmacotherapy. Despite being approximately one-tenth the size of a conventional antibody, they retain similar specificity and affinity to conventional antibodies and are much easier to clone and manipulate. Their unique properties such as small size, high stability, strong antigen binding affinity, water solubility, and natural origin make them suitable for the development of biopharmaceuticals and nanoreagents. The present review aims to describe the main structural and biochemical characteristics of these antibodies and to provide an update on their applications in research, biotechnology, and medicine. For this purpose, an exhaustive search of the biomedical literature was performed in the following databases: Medline (PubMed), Google Scholar, and ScienceDirect. Meta-analyses, observational studies, review articles, and clinical guidelines were reviewed. Only original articles were considered to assess the quality of the evidence., (© 2021 Institute of Bioorganic Chemistry, Polish Academy of Sciences.)

COVID-19 is currently having major short run effects with possible serious long run implications for the environment and the management of natural resources in Latin America. We discuss the possible effects of the pandemic on air pollution, deforestation and other relevant environmental dimensions across the region. With contributions from environmental economists from eight countries, we give an overview of the initial and expected environmental effects of this health crisis. We discuss potential effects on environmental regulations, possible policy interventions, and an agenda for future research for those interested in the design and evaluation of environmental policies relevant for the Latin American context., (© Springer Nature B.V. 2020.)

Protected areas (PAs) are the leading tools to conserve forests. However, given their mixed effectiveness, we want to know when they have impacts internally and, if they do, when they have spillovers. Political economy posits roles for the level of government. One hypothesis is that federal PAs avoid more internal deforestation than state PAs since federal agencies consider gains for other jurisdictions. Such political differences as well as economic mechanisms can cause PA spillovers to vary greatly, even from "leakage," more deforestation elsewhere, to "blockage," less deforestation elsewhere. We examine internal impacts and local spillovers for Brazilian Amazon federal and state agencies. Outside the region's "arc of deforestation," we confirm little internal impact and show no spillovers. In the "arc," we test impacts by state, as states are large and feature considerably different dynamics. For internal impacts, estimates for federal PAs and indigenous lands are higher than for state PAs. For local spillover impacts, estimates for most arc states either are not significant or are not robust; however, for Pará, federal PAs and indigenous lands feature both internal impacts and local spillovers. Yet, the spillovers in Pará go in opposite directions across agencies, leakage for indigenous lands but blockage for federal PAs, suggesting a stronger external signal from the environmental agency. Across all these tools, only federal PAs lower deforestation internally and nearby. Results suggest that agencies' objectives and capacities are critical parts of the contexts for conservation strategies., Competing Interests: The authors declare no conflict of interest.

Protected areas (PAs) are a prominent approach to maintaining and enhancing biodiversity and ecosystem services. A critical question for safeguarding these resources is how PA governance processes and management structures influence their effectiveness. We conduct an impact evaluation of 12 PAs in three Central American countries to assess how processes in management restrictions, management capacity, and decentralization affect the annual change in the satellite-derived Normalized Difference Vegetation Index (NDVI). NDVI varies with greenness that relates to plant production, biomass, and important ecosystem functions related to biodiversity and ecosystem services such as water quality and carbon storage. Any loss of vegetation cover in the form of deforestation or degradation would show up as a decrease in NDVI values over time and gains in vegetation cover and regeneration as an increase in NDVI values. Management restriction categories are based on international classifications of strict versus multiple-use PAs, and capacity and decentralization categories are based on key informant interviews of PA managers. We use matching to create a counterfactual of non-protected observations and a matching estimator and regression to estimate treatment effects of each sub-sample. On average, strict and multiple-use PAs have a significant and positive effect on NDVI compared to non-protected land uses. Both high and low decentralized PAs also positively affect NDVI. High capacity PAs have a positive and significant effect on NDVI, while low capacity PAs have a negative effect on NDVI. Our findings advance knowledge on how governance and management influence PA effectiveness and suggest that capacity may be more important than governance type or management restrictions in maintaining and enhancing NDVI. This paper also provides a guide for future studies to incorporate measures of PA governance and management into impact evaluations., Competing Interests: The authors have declared that no competing interests exist.

In order to ensure the provision of goods and services from forests, many governments have promoted less-traditional conservation initiatives such as programs of payments for ecosystem services called, more broadly, direct payments for conservation. The Socio Bosque Program (SBP) is a governmental program in Ecuador that directly provides economic incentives to rural families and local and indigenous communities who have voluntarily agreed to comply with some conservation activities. An impact evaluation method (matching) was used to assess the impact of the SBP between 2008 and 2014. This study revealed that on average, the SBP reduced deforestation by 1.5% in those forests that received the SBP's direct payment. These forests would have been deforested if the SBP had not been implemented. Assessment of the impact of the SBP on individual and collective contracts, using the matching method, revealed that 3.4% and roughly 1% of the forest would have been deforested in the absence of the program, respectively. In other words, the protected area in the collective SBP was 1,247,500 ha and, if the SBP had not been implemented, an area of 11,227 ha would have been lost between 2008 and 2014. The 165,700 ha protected by the individual SBP, it was estimated that 5,733 ha were not deforested due to the implementation of the conservation program. Conventional estimates of the impact of the SBP tend to overestimate avoided deforestation because they do not control for observable covariates that correlate with or affect both SBP participation and deforestation. The conclusions are robust, even given potential hidden biases. The present study demonstrated that the SBP serves to mitigate the effects of climate change, especially with those contracts that are intended for individual owners., Competing Interests: The authors have declared that no competing interests exist.

The uptake and destruction of bacteria by phagocytic cells is an essential defense mechanism in metazoans. To identify novel genes involved in the phagocytosis of Staphylococcus aureus , a major human pathogen, we assessed the phagocytic capacity of adult blood cells (hemocytes) of the fruit fly, Drosophila melanogaster, by testing several lines of the Drosophila Genetic Reference Panel. Natural genetic variation in the gene RNA-binding Fox protein 1 ( Rbfox1 ) correlated with low phagocytic capacity in hemocytes, pointing to Rbfox1 as a candidate regulator of phagocytosis. Loss of Rbfox1 resulted in increased expression of the Ig superfamily member Down syndrome adhesion molecule 4 ( Dscam4 ). Silencing of Dscam4 in Rbfox1-depleted blood cells rescued the fly's cellular immune response to S. aureus , indicating that downregulation of Dscam4 by Rbfox1 is critical for S. aureus phagocytosis in Drosophila To our knowledge, this study is the first to demonstrate a link between Rbfox1, Dscam4, and host defense against S. aureus ., (Copyright © 2018 by The American Association of Immunologists, Inc.)

Scientists building the Tree of Life face an overwhelming challenge to categorize phenotypes (e.g., anatomy, physiology) from millions of living and fossil species. This biodiversity challenge far outstrips the capacities of trained scientific experts. Here we explore whether crowdsourcing can be used to collect matrix data on a large scale with the participation of nonexpert students, or "citizen scientists." Crowdsourcing, or data collection by nonexperts, frequently via the internet, has enabled scientists to tackle some large-scale data collection challenges too massive for individuals or scientific teams alone. The quality of work by nonexpert crowds is, however, often questioned and little data have been collected on how such crowds perform on complex tasks such as phylogenetic character coding. We studied a crowd of over 600 nonexperts and found that they could use images to identify anatomical similarity (hypotheses of homology) with an average accuracy of 82% compared with scores provided by experts in the field. This performance pattern held across the Tree of Life, from protists to vertebrates. We introduce a procedure that predicts the difficulty of each character and that can be used to assign harder characters to experts and easier characters to a nonexpert crowd for scoring. We test this procedure in a controlled experiment comparing crowd scores to those of experts and show that crowds can produce matrices with over 90% of cells scored correctly while reducing the number of cells to be scored by experts by 50%. Preparation time, including image collection and processing, for a crowdsourcing experiment is significant, and does not currently save time of scientific experts overall. However, if innovations in automation or robotics can reduce such effort, then large-scale implementation of our method could greatly increase the collective scientific knowledge of species phenotypes for phylogenetic tree building. For the field of crowdsourcing, we provide a rare study with ground truth, or an experimental control that many studies lack, and contribute new methods on how to coordinate the work of experts and nonexperts. We show that there are important instances in which crowd consensus is not a good proxy for correctness., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Several shrimp species from the clade Penaeidae are farmed industrially for human consumption, and this farming has turned shrimp into the largest seafood commodity in the world. The species that are in demand for farming are an anomaly within their clade because they grow to much larger sizes than other members of Penaeidae. Here we trace the evolutionary history of the anomalous farmed shrimp using combined data phylogenetic analysis of living and fossil species. We show that exquisitely preserved fossils of †Antrimpos speciosus from the Late Jurassic Solnhofen limestone belong to the same clade as the species that dominate modern farming, dating the origin of this clade to at least 145 mya. This finding contradicts a much younger Late Cretaceous age (ca. 95 mya) previously estimated for this clade using molecular clocks. The species in the farmed shrimp clade defy a widespread tendency, by reaching relatively large body sizes despite their warm water lifestyles. Small body sizes have been shown to be physiologically favored in warm aquatic environments because satisfying oxygen demands is difficult for large organisms breathing in warm water. Our analysis shows that large-bodied, farmed shrimp have more gills than their smaller-bodied shallow-water relatives, suggesting that extra gills may have been key to the clade's ability to meet oxygen demands at a large size. Our combined data phylogenetic tree also suggests that, during penaeid evolution, the adoption of mangrove forests as habitats for young shrimp occurred multiple times independently.

The importance of microbiomes in health and disease is now well appreciated. New work from Sansone and colleagues adds to this understanding by showing that gut microbes are key for the local induction of an ERK-dependent antiviral response in flies., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The leading policy to conserve forest is protected areas (PAs). Yet, PAs are not a single tool: land users and uses vary by PA type; and public PA strategies vary in the extent of each type and in the determinants of impact for each type, i.e. siting and internal deforestation. Further, across regions and time, strategies respond to pressures (deforestation and political). We estimate deforestation impacts of PA types for a critical frontier, the Brazilian Amazon. We separate regions and time periods that differ in their deforestation and political pressures and document considerable variation in PA strategies across regions, time periods and types. The siting of PAs varies across regions. For example, all else being equal, PAs in the arc of deforestation are relatively far from non-forest, while in other states they are relatively near. Internal deforestation varies across time periods, e.g. it is more similar across the PA types for PAs after 2000. By contrast, after 2000, PA extent is less similar across PA types with little non-indigenous area created inside the arc. PA strategies generate a range of impacts for PA types--always far higher within the arc--but not a consistent ranking of PA types by impact., (© 2015 The Author(s).)

Protected areas are the leading forest conservation policy for species and ecoservices goals and they may feature in climate policy if countries with tropical forest rely on familiar tools. For Brazil's Legal Amazon, we estimate the average impact of protection upon deforestation and show how protected areas' forest impacts vary significantly with development pressure. We use matching, i.e., comparisons that are apples-to-apples in observed land characteristics, to address the fact that protected areas (PAs) tend to be located on lands facing less pressure. Correcting for that location bias lowers our estimates of PAs' forest impacts by roughly half. Further, it reveals significant variation in PA impacts along development-related dimensions: for example, the PAs that are closer to roads and the PAs closer to cities have higher impact. Planners have multiple conservation and development goals, and are constrained by cost, yet still conservation planning should reflect what our results imply about future impacts of PAs.

We estimate the effects on deforestation that have resulted from policy interactions between parks and payments and between park buffers and payments in Costa Rica between 2000 and 2005. We show that the characteristics of the areas where protected and unprotected lands are located differ significantly. Additionally, we find that land characteristics of each of the policies and of the places where they interact also differ significantly. To adequately estimate the effects of the policies and their interactions, we use matching methods. Matching is implemented not only to define adequate control groups, as in previous research, but also to define those groups of locations under the influence of policies that are comparable to each other. We find that it is more effective to locate parks and payments away from each other, rather than in the same location or near each other. The high levels of enforcement inside both parks and lands with payments, and the presence of conservation spillovers that reduce deforestation near parks, significantly reduce the potential impact of combining these two policies.

The need for better control of infectious diseases in shrimp aquaculture and the ecological importance of crustacea in marine ecosystems have prompted interest in the study of crustacean immune systems, particularly those of shrimp. As shrimp and other crustacea are poorly understood from the immunological point of view, functional genomic and proteomic approaches have been applied as a means of quickly obtaining molecular information regarding immune responses in these organisms. In this article, a series of results derived from transcriptomic and proteomic studies in shrimp (Litopenaeus vannamei) are discussed. Expressed Sequence Tag analysis, differential expression cloning through Suppression Subtractive Hybridization, expression profiling using microarrays, and proteomic studies using mass spectrometry, have provided a wealth of useful data and opportunities for new avenues of research. Examples of new research directions arising from these studies in shrimp include the molecular diversity of antimicrobial effectors, the role of double stranded RNA as an inducer of antiviral immunity, and the possible overlap between antibacterial and antiviral responses in the shrimp.

Antimicrobial peptides are an essential component of the innate immune system of most organisms. Expressed sequence tag analysis from various shrimp (Litopenaeus vannamei) tissues revealed transcripts corresponding to two distinct sequences (LvALF1 and LvALF2) with strong sequence similarity to anti-lipopolysaccharide factor (ALF), an antimicrobial peptide originally isolated from the horseshoe crab Limulus polyphemus. Full-length clones contained a 528bp transcript with a predicted open reading frame coding for 120 amino acids in LvALF1, and a 623bp transcript with a predicted open reading frame coding for 93 amino acids in LvALF2. A reverse genetic approach was implemented to study the in vivo role of LvALF1 in protecting shrimp from bacterial, fungal and viral infections. Injection of double-stranded RNA (dsRNA) corresponding to the LvALF1 message resulted in a significant reduction of LvALF1 mRNA transcript abundance as determined by qPCR. Following knockdown, shrimp were challenged with low pathogenic doses of Vibrio penaeicida, Fusarium oxysporum or white spot syndrome virus (WSSV) and the resulting mortality curves were compared with controls. A significant increase of mortality in the LvALF1 knockdown shrimp was observed in the V. penaeicida and F. oxysporum infections when compared to controls, showing that this gene has a role in protecting shrimp from both bacterial and fungal infections. In contrast, LvALF1 dsRNA activated the sequence-independent innate anti-viral immune response giving increased protection from WSSV infection.

Infectious disease constitutes a major obstacle to the sustainability of shrimp aquaculture worldwide and a significant threat to natural populations of shrimp and other crustacea. The study of the shrimp immune system, including the response to viral infection, has been hampered by a relative lack of molecular genetic information and of tools suitable for high-throughput assessment of gene expression. In this report, the generation of a cDNA microarray encompassing 2,469 putative unigenes expressed in gills, circulating hemocytes, and hepatopancreas of Litopenaeus vannamei is described. The unigenes printed on the microarray were derived from the analyses of 7,021 expressed sequence tags obtained from standard cDNA libraries as well as from libraries generated by suppression subtractive hybridization, after challenging shrimp with a variety of immune stimuli. The general utility of the cDNA microarray was demonstrated by interrogating the array with labeled RNA from four different shrimp tissues (gills, hemocytes, hepatopancreas, and muscle) and by analyzing the transcriptomic response of shrimp to a lethal challenge with white spot syndrome virus. Our results indicate that white spot syndrome virus infection upregulates (in the hepatopancreas) genes encoding known and potential antimicrobial effectors, while some genes involved in protection from oxidative stress were found to be downregulated by the virus.

Double-stranded RNA (dsRNA) is a common virus-associated molecular pattern and a potent inducer of antiviral responses in many organisms. While it is clear that the specific RNA interference (RNAi) response, a phenomenon triggered by dsRNA, serves antiviral functions in invertebrates, innate (non-specific) antiviral immune reactions induced by dsRNA (e.g. the Interferon response) have long been thought to be restricted to vertebrates. Recent work in an underappreciated experimental model, the penaeid shrimp, is challenging these traditional distinctions, by demonstrating the existence of both innate (non sequence-specific) and RNAi-related (sequence-specific) antiviral phenomena in crustacea. Here we discuss the evidence for this bivalent role of dsRNA in the initiation of antiviral responses in shrimp, and present new data that suggest that the antiviral functions of the shrimp RNAi machinery have imposed selective pressures on an evolving viral pathogen. These findings open the door for the discovery of novel mechanisms of innate immunity, and provide a basis for the future development of strategies to control viral diseases in the commercially important penaeid shrimp.

Ecogenomics is a convenient descriptor for the application of advanced molecular technologies to studies of organismal responses to environmental challenges in their natural settings. The development of molecular tools to survey changes in the transcript profile of thousands of genes has presented scientists with enormous analytical challenges. In the main, these center about the reduction of massively paralleled data to statistics or indices comprehensible to the human mind. Historically, scientists have used linear statistics such as ANOVA to accomplish this task, but the sheer volume of information available from microarrays severely limits this approach. In addition, important information in microarrays may not reside solely in the up or down regulation of individual genes, but rather in their dynamic, and probably nonlinear, interactions. In this presentation, we will explore alternative approaches to extracting of these signals using artificial neural networks and fractal geometry. The goal is to produce predictive models of gene dynamics in individuals and populations under environmental stress and reduce the number of genes that must be surveyed in order to recover transcript profile patterns of environmental challenges.

Multiple small-scale transcriptome studies have been undertaken for various members of the Penaeidae. Penaeid shrimp are important both as members of diverse ecosystems around the world and for their importance as commercial commodities. Of the many shrimps, the most important from this family is the Pacific whiteleg shrimp, Litopenaeus vannamei, as it is the primary shrimp used in worldwide aquaculture. The sequencing and analysis of 13 656 expressed sequence tags (ESTs) from this species is presented. ESTs were derived from multiple tissue-specific cDNA libraries with an emphasis being placed on those tissues with predicted immune function. Assembly of the sequences into non-overlapping clusters yielded 7466 putative unigenes (1981 contigs and 5485 singletons). Multiple approaches were taken to assign putative function to each transcript; sequence homology searches using BLASTX (Basic Local Alignment Search Tool: Translated query versus protein database) of the National Center for Biotechnology Information's (NCBI) GenBank Database and Gene Ontology annotation, and still a significant portion of the shrimp ESTs (62%) had no homology with known proteins in the public databases. The sequence and complete annotation of all ESTs is available at www.marinegenomics.org, a publicly accessible database. In addition to providing the basic resources for microarray construction, transcript profiling, and novel gene discovery, this study constitutes the largest combined analysis of ESTs from any shrimp species and is a prelude to an even larger effort aimed at identifying and depleting highly redundant genes from shrimp cDNA libraries toward the goal of sequencing 100 000 shrimp ESTs.

White Spot Syndrome Virus (WSSV) is a highly pathogenic and prevalent virus affecting crustacea. A number of WSSV envelope proteins, including vp28, have been proposed to be involved in viral infectivity based on the ability of specific antibodies to attenuate WSSV-induced mortality in vivo. In the present study, a series of monoclonal and polyclonal antibodies targeting vp28 were tested for their ability to neutralize WSSV infectivity, with the purpose of identifying epitopes potentially involved in vp28-mediated infection of shrimp. Surprisingly, when used as protein A-purified immunoglobulin, none of the antibodies tested were capable of inhibiting WSSV infectivity. This included one polyclonal preparation that has been previously shown to inactivate WSSV, when used as whole rabbit serum. Moreover, strong inactivation of WSSV by some rabbit sera was observed, in a manner independent of anti-vp28 antibodies. These results underscore the problems associated with using heterogeneous reagents (e.g. whole rabbit antiserum) in viral neutralization experiments aimed at defining proteins involved in infection by WSSV. In light of this, the potential of anti-vp28 antibodies to specifically neutralize WSSV should be reconsidered.

Double-stranded RNA (dsRNA) is a common by-product of viral infections and a potent inducer of innate antiviral immune responses in vertebrates. In the marine shrimp Litopenaeus vannamei, innate antiviral immunity is also induced by dsRNA in a sequence-independent manner. In this study, the hypothesis that dsRNA can evoke not only innate antiviral immunity but also a sequence-specific antiviral response in shrimp was tested. It was found that viral sequence-specific dsRNA affords potent antiviral immunity in vivo, implying the involvement of RNA interference (RNAi)-like mechanisms in the antiviral response of the shrimp. Consistent with the activation of RNAi by virus-specific dsRNA, endogenous shrimp genes could be silenced in a systemic fashion by the administration of cognate long dsRNA. While innate antiviral immunity, sequence-dependent antiviral protection, and gene silencing could all be induced by injection of long dsRNA molecules, injection of short interfering RNAs failed to induce similar responses, suggesting a size requirement for extracellular dsRNA to engage antiviral mechanisms and gene silencing. We propose a model of antiviral immunity in shrimp by which viral dsRNA engages not only innate immune pathways but also an RNAi-like mechanism to induce potent antiviral responses in vivo.

Background: The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org., Description: The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences) that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC) editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB., Conclusion: The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.