Fishery Ecosystem Dynamics

2020 ◽  
Author(s):  
Michael J. Fogarty ◽  
Jeremy S. Collie
Keyword(s):  
Aquatic Ecosystems ◽  
Large Scale ◽  
Human Impacts ◽  
Ecosystem Dynamics ◽  
Ecosystem Structure ◽  
Ecological Processes ◽  
Scale Removal ◽  
Sustainable Resource Management ◽  
Broad Array ◽  
Traditional Approaches

This book provides an integrated framework for the quantitative analysis of exploited aquatic ecosystems, tracing the critical linkages between fundamental ecological processes and their implications for sustainable resource management. Examples are drawn from freshwater and marine ecosystems throughout the world. Fishery ecosystems have historically been subject to a broad array of human interventions, ranging from large-scale removal of biomass to deliberate attempts at ecosystem engineering involving species introductions, habitat alteration, and selective reorganization of ecosystem structure. Traditional approaches to fisheries analysis and management focus on extraction of resources viewed in isolation from the broader ecosystem setting. Further, these approaches typically are predicated on assumptions of “well-behaved” dynamical properties characterized by stable equilibrium properties. This book explores a broader range of possibilities concerning human impacts on aquatic ecosystems. It places software tools in the hands of students and professionals in an electronic supplement. Modeling and statistical programs in R and other platforms are provided to assist in the transition from concept to practical application.

Recent Progress in Machine Learning-based Prediction of Peptide Activity for Drug Discovery

2019 ◽  
Vol 19 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Qihui Wu ◽  
Hanzhong Ke ◽  
Dongli Li ◽  
Qi Wang ◽  
Jiansong Fang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Large Scale ◽  
Recent Progress ◽  
High Specificity ◽  
Learning Approaches ◽  
Anticancer Peptides ◽  
The Past ◽  
Traditional Approaches ◽  
Large Scale Screening

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.

scholarly journals Agricultural Conservation Practices and Aquatic Ecological Responses

Water ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 1687
Author(s):  
Richard E. Lizotte ◽  
Peter C. Smiley ◽  
Robert B. Gillespie ◽  
Scott S. Knight
Keyword(s):  
Aquatic Ecosystems ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Soil Health ◽  
Conservation Agriculture ◽  
Agricultural Runoff ◽  
The United States ◽  
Ecosystem Structure ◽  
Ecological Responses ◽  
And Function

Conservation agriculture practices (CAs) have been internationally promoted and used for decades to enhance soil health and mitigate soil loss. An additional benefit of CAs has been mitigation of agricultural runoff impacts on aquatic ecosystems. Countries across the globe have agricultural agencies that provide programs for farmers to implement a variety of CAs. Increasingly there is a need to demonstrate that CAs can provide ecological improvements in aquatic ecosystems. Growing global concerns of lost habitat, biodiversity, and ecosystem services, increased eutrophication and associated harmful algal blooms are expected to intensify with increasing global populations and changing climate. We conducted a literature review identifying 88 studies linking CAs to aquatic ecological responses since 2000. Most studies were conducted in North America (78%), primarily the United States (73%), within the framework of the USDA Conservation Effects Assessment Project. Identified studies most frequently documented macroinvertebrate (31%), fish (28%), and algal (20%) responses to riparian (29%), wetland (18%), or combinations (32%) of CAs and/or responses to eutrophication (27%) and pesticide contamination (23%). Notable research gaps include better understanding of biogeochemistry with CAs, quantitative links between varying CAs and ecological responses, and linkages of CAs with aquatic ecosystem structure and function.

scholarly journals Enzyme-catalyzed biodegradation of penicillin fermentation residues by β-lactamase OtLac from Ochrobactrum tritici

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Peng Wang ◽  
Chen Shen ◽  
Qinqin Cong ◽  
Kaili Xu ◽  
Jialin Lu
Keyword(s):  
Large Scale ◽  
In Vitro Study ◽  
Scale Removal ◽  
E Coli ◽  
Penicillin V ◽  
Highly Active ◽  
Steady State Kinetics ◽  
Biodegradation Process ◽  
Km Value

Abstract Background Biodegradation of antibiotics is a promising method for the large-scale removal of antibiotic residues in the environment. However, the enzyme that is involved in the biodegradation process is the key information to be revealed. Results In this study, the beta-lactamase from Ochrobactrumtritici that mediates the biodegradation of penicillin V was identified and characterized. When searching the proteins of Ochrobactrumtritici, the β-lactamase (OtLac) was identified. OtLac consists of 347 amino acids, and predicted isoelectric point is 7.0. It is a class C β-lactamase according to BLAST analysis. The coding gene of OtLac was amplified from the genomic DNA of Ochrobactrumtritici. The OtLac was overexpressed in E. coli BL21 (DE3) and purified with Ni2+ column affinity chromatography. The biodegradation ability of penicillin V by OtLac was identified in an in vitro study and analyzed by HPLC. The optimal temperature for OtLac is 32 ℃ and the optimal pH is 7.0. Steady-state kinetics showed that OtLac was highly active against penicillin V with a Km value of 17.86 μM and a kcat value of 25.28 s−1 respectively. Conclusions OtLac demonstrated biodegradation activity towards penicillin V potassium, indicating that OtLac is expected to degrade penicillin V in the future.

Going with the flow: global warming and the challenge of sustaining river ecosystems in monsoonal Asia

2007 ◽  
Vol 7 (2) ◽  
pp. 69-80 ◽  
Author(s):  
D. Dudgeon
Keyword(s):  
Global Warming ◽  
Human Impacts ◽  
Habitat Destruction ◽  
Dispersal Ability ◽  
Suitable Habitat ◽  
Hydrologic Alteration ◽  
Ecological Processes ◽  
Ecosystem Integrity ◽  
River Ecosystems ◽  
The Rich

River ecosystems in monsoonal Asia are experiencing human impacts to the detriment of the rich biodiversity they support. Threats include hydrologic alteration, pollution, habitat destruction, overexploitation, and invasive exotic species. Global warming will cause further changes to river ecosystems, and may act synergistically with other threat factors. Significant upward or northward range adjustments by the freshwater biota will be necessary to cope with rising temperatures, but there will be significant constraints upon dispersal ability and availability of suitable habitat for many organisms. Global warming will exacerbate existing impacts of hydrologic alteration because of the adaptive human responses that will be engendered by changes in climate and runoff, particularly dams constructed for hydropower generation, flood protection, water storage, and irrigation. The consequences of further hydrologic alteration and habitat fragmentation will be profound, since almost all ecological processes, material transfers and life-cycle events in the rivers of monsoonal Asia are mediated or controlled by flow. Thus a change in the timing or amounts of flow changes everything. Collaborative research to determine the environmental allocation of water flow needed to maintain ecosystem integrity and sustain biodiversity in the human-dominated rivers of monsoonal Asia should be a priority for ecologists, engineers and water-resource managers.

scholarly journals An Estimation of Fish Biomass and Attached Organisms beneath Oyster Rafts in Hiroshima Bay, Japan

2021 ◽  
Vol 324 ◽  
pp. 03013
Author(s):  
Wahyudin Wahyudin ◽  
Tamiji Yamamoto
Keyword(s):  
Large Scale ◽  
Fish Habitat ◽  
Food Chains ◽  
Ecosystem Structure ◽  
Fish Production ◽  
Underwater Video ◽  
Oyster Culture ◽  
Video Cameras ◽  
Black Seabream ◽  
Material Cycles

Hiroshima Bays is top production approximately 60% of oyster production in Japan. For cultivate of oyster, fishermen use hanging rafts. A thousand of raft is hanging during 2-3 years in the bay. Large-scale oyster culture may change the ecosystem structure and material cycles in the bay through the filtration of particulate matter by oysters and other associated animals. This study described the community structure of marine organisme in terms of fishes surrounding and animal attached on oyster rafts. Field observation was carried out from 2016 to 2019 at oyster farming in Hiroshima Bay. Oyster production and provisioning for the fish habitat were also evaluated by placing underwater video cameras beneath oyster culture rafts. The result showed that black seabream was high biomass and oyster it shelf was bigger bioyster for animal attached on oyster raft. The number of individual, mussel is most abundance of animal attach on oyster raft with ratio 9:1 than number of oyster. Maintaining oyster culture is important not only for maintaining oyster production, but also for maintaining fish production by enhancing material cycles through the paths in the food chains of Hiroshima Bay under oligotrophic conditions.

scholarly journals New kid on the block: Research of alpine-lake macroinvertebrates in the Tatra Mountains enhanced by DNA barcoding and metabarcoding

2021 ◽  
Vol 4 ◽  
Author(s):  
Ondrej Vargovčík ◽  
Zuzana Čiamporová-Zaťovičová ◽  
Fedor Čiampor Jr
Keyword(s):  
Large Scale ◽  
Environmental Changes ◽  
Human Impacts ◽  
Sampling Error ◽  
Alpine Lakes ◽  
Alpine Lake ◽  
Tatra Mountains ◽  
Aquatic Communities ◽  
Wide Range ◽  
The Tatra Mountains

State of ecosystems and biodiversity protection are becoming the key interests for modern society due to climate change and negative human impacts (Leese 2018). Environmental changes in freshwaters are indicated also by benthic communities, especially in sensitive ecosystems like alpine lakes (Fjellheim 2009). Moreover, remoteness and isolation of alpine lakes make them a source of biodiversity, which is worth conserving (Hamerlík 2014). A promising tool for efficient large-scale monitoring of aquatic communities is DNA metabarcoding (Leese 2018). In this study, we applied metabarcoding to analyse macrozoobenthos of 12 lakes in the Tatra Mountains, using benthic bulk samples and eDNA filtered from water (Fig. 1). In compliance with recent publications, eDNA amplified with BF3/BR2 primers resulted in high percentage of non-invertebrate reads (Leese 2021). Based on in silico tests with the obtained sequences, we confirm that the recently developed EPTDr2n primer enables minimizing non-target amplification even with eDNA filtered from alpine-lake water (Elbrecht and Leese 2017). This ability is facilitated by 3’ end of the primer and we observed the two important mismatches in non-target sequences from our study (Leese 2021). Thus, our future analyses of eDNA (and bulk-sample fixative) will benefit from the new primer. Concerning bulk samples, a wide range of invertebrate taxa was assigned to the OTUs and they showed good congruence with previous studies using morphological determination (e.g. Krno 2006). Certain differences with (and among) the previous records per lake were observed, which could suggest ecological changes, but at the moment the influence of sampling error cannot be excluded. In eDNA, several taxa were congruent with the previous records, but their amount and read abundance was considerably lower due to non-target amplification. Apart from that, filling gaps in barcoding databases remains one of our priorities, as identification to species or genus level was not yet possible for some invertebrate OTUs. In addition, we subjected the NGS data to denoising and abundance-filtering in order to explore haplotype-level diversity (Andújar 2021). Although more comprehensive conclusions will be possible only after obtaining data from more lakes and years, already the two metabarcoding experiments presented here enabled us to efficiently detect within-species genetic diversity and identify a large variety of taxa, including groups that would otherwise be omitted or very challenging to identify. This underlines the potential of DNA methods to provide valuable ecological and biodiversity data across the tree of life for modern biomonitoring. This study was realized with support from VEGA 2/0030/17 and VEGA 2/0084/21.

scholarly journals Human impacts and Anthropocene environmental change at Lake Kutubu, a Ramsar wetland in Papua New Guinea

2021 ◽  
Vol 118 (40) ◽  
pp. e2022216118 ◽  
Author(s):  
Kelsie E. Long ◽  
Larissa Schneider ◽  
Simon E. Connor ◽  
Niamh Shulmeister ◽  
Janet Finn ◽  
...  
Keyword(s):  
Mineral Resource ◽  
Environmental Change ◽  
Papua New Guinea ◽  
Human Impacts ◽  
Wetland Management ◽  
New Guinea ◽  
Ecosystem Dynamics ◽  
Resource Extraction ◽  
Human Populations ◽  
Ramsar Wetland

The impacts of human-induced environmental change that characterize the Anthropocene are not felt equally across the globe. In the tropics, the potential for the sudden collapse of ecosystems in response to multiple interacting pressures has been of increasing concern in ecological and conservation research. The tropical ecosystems of Papua New Guinea are areas of diverse rainforest flora and fauna, inhabited by human populations that are equally diverse, both culturally and linguistically. These people and the ecosystems they rely on are being put under increasing pressure from mineral resource extraction, population growth, land clearing, invasive species, and novel pollutants. This study details the last ∼90 y of impacts on ecosystem dynamics in one of the most biologically diverse, yet poorly understood, tropical wetland ecosystems of the region. The lake is listed as a Ramsar wetland of international importance, yet, since initial European contact in the 1930s and the opening of mineral resource extraction facilities in the 1990s, there has been a dramatic increase in deforestation and an influx of people to the area. Using multiproxy paleoenvironmental records from lake sediments, we show how these anthropogenic impacts have transformed Lake Kutubu. The recent collapse of algal communities represents an ecological tipping point that is likely to have ongoing repercussions for this important wetland’s ecosystems. We argue that the incorporation of an adequate historical perspective into models for wetland management and conservation is critical in understanding how to mitigate the impacts of ecological catastrophes such as biodiversity loss.

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