Otolith Shape Analysis as a Tool for Species Identification and Studying the Population Structure of Different Fish Species

An analysis and a comparison of the methods of geometric morphometrics as applied to fish species identification and to studies on the population structure of fish stocks based on peculiarities of the otolith shape are performed. A review of the geometric morphometric methods used in studies on fish otoliths is provided. The results of our own research on possible utilization of elliptical Fourier analysis for species identification are also described.     

Molecular tools for the detection and identification of Ichthyobodo spp. (Kinetoplastida), important fish parasites

Ichthyobodo spp. are ectoparasitic flagellates of fish that may cause disease (ichthyobodosis), a common problem affecting the aquaculture industry worldwide. Ichthyobodosis in farmed fish is often associated with a range of other infectious agents and diagnosis in for example gill disease may be difficult. Sensitive and effective methods for detection and identification of Ichthyobodo spp. are needed to aid diagnosis of ichthyobodosis and epizootiological studies on Ichthyobodo spp. We have designed a specific quantitative real-time PCR assay targeting SSU rDNA for the detection of Ichthyobodo spp. infections. Also, several novel primer sets are presented for use in identification of Ichthyobodo spp. through PCR and sequencing. These PCR methods have been optimized and tested on samples from wild caught and farmed fish from different geographical areas in Norway. The real-time PCR assay has been tested for sensitivity and efficiency, and we present data demonstrating its use for absolute quantification of Ichthyobodo salmonis in tissue samples through RT-qPCR and qPCR. We demonstrate the use of the described set of molecular tools for the detection and sequencing of Ichthyobodo spp. from farmed and wild fish, and also show that they may aid the discovery of new Ichthyobodo species. The detection of light Ichthyobodo spp. infections through microscopy is time consuming and less sensitive compared to PCR methods. Initial real-time PCR testing and subsequent sequencing of positive samples is a powerful method that will increase diagnostic precision, aid carrier detection and promote species discoveries in the Ichthyobodonidae. Our preliminary observations indicate a high Ichthyobodo spp. diversity.     

DNA barcoding reveals the temporal community composition of drifting fish eggs in the lower Hongshui River,China

Determining the temporal community composition of fish eggs in particular regions and understanding the reproductive times of regional fish taxa are key aspects of the management and regulation of regional fish stocks. However, it is extremely difficult to accurately identify fish eggs due to the absence of diagnostic morphological characters. We sampled fish eggs in the lower Hongshuihe River (an upper mainstem of the Pearl River) between May and September 2020. We then used DNA barcoding to determine the species composition of the egg pool and to predict the spawning periods of the identified species. A total of 641 eggs and 17 larvae were chosen for molecular identification; 397 eggs and 17 larvae yielded high‐quality barcoding sequences. The high failure rate (~38%) was most likely due to long‐term storage in low concentrations of ethanol prior to molecular analysis. We successfully classified 392 eggs into 10 species and 13 larvae into four species using public databases. Most of the species identified in the egg pool were small and/or benthic, and migratory species were rare. This may partially reflect the adverse effects of hydropower cascade development in this river section. We also found that spawning periods tended to be species‐specific. Our study provides a reference for the conservation and management of regional fishery stocks.     

Co-occurrence of viral and bacterial pathogens in disease outbreaks affecting newly cultured sparid fish.

Several microbial disease outbreaks in farm stocks of newly cultured sparid fish species, such as common seabream, redbanded seabream, and white seabream, were recorded from 2004 to 2006. This study describes the isolation and characterization of the potential causative agents, either bacteria or viruses, of these outbreaks. The isolated bacterial strains were characterized according to traditional taxonomical analyses and sequencing of a 16S rDNA fragment. Most bacteria were identified as Vibrio spp. and Photobacterium damselae subsp. damselae. The development of cytopathic effects (CPE) on different fish cell lines, the application of specific nested-PCR tests for infectious pancreatic necrosis virus (IPNV), viral nervous necrosis virus (VNNV) and viral hemorrhagic septicemia virus (VHSV), and subsequent sequence analyses were used for virus detection and identification. VNNV, related to the striped jack neural necrosis virus (SJNNV) genotype, and VHSV, related to the genotype Ia, were the only viruses detected. VNNV was isolated from the three fish species under study in five different outbreaks, whereas VHSV was isolated from common seabream and white seabream during two of these outbreaks. IPNV was not detected in any case.     

Western equine and St. Louis encephalitis in man,California, 1945-1950

A large group of etiologic agents, some known and some unknown, produce in man a clinical syndrome now labeled "infectious encephalitis."The separation, from this larger group, of single disease entities which cause similar clinical symptoms is possible, but calls for diagnostic acumen plus supporting laboratory evidence. Two etiologically specific entities, western equine encephalitis and St. Louis encephalitis, are frequently encountered in rather well-defined areas of California, the Central Valley and Imperial Valley; and there is a definite seasonal pattern of occurrence-June through October. There are certain guides that are helpful in differential diagnosis. Establishing a diagnosis on the basis of clinical evidence is difficult. Laboratory studies are of great importance not only for diagnosis in the individual case but for advancement of etiology. Specimens are worthless unless taken at proper intervals and submitted by methods described. It is probable that encephalitides caused by still unknown agents exist in California. The isolation and identification of new encephalitogenic viral agents will depend in large measure upon the submission by physicians of suitable specimens from patients with central nervous system disease in which the cause is obscure.     

The possibilities of improving catchable fish stocks in lakes undergoing eutrophication

The area of Mazurian Lakeland is the biggest lake concentration in Middle Europe. Its lakes are subjected to various man-made impacts and disturbances, resulting in many changes in the aquatic environment and the fish stocks. Most frequently these changes are typical of the process of accelerated eutrophication, and are connected with undesirable succession in the fish stocks. Generally, predatory species, which naturally regulate the stock and maintaiil its balance, disappear from the environment, as do other valuable fish species, e.g. coregonids. At the same time food resources (weed fishes, plankton) for those species develop abundantly.
Assessment of the management of lakes by one of the State Lake Fish Farms located in Mazurian Lakeland is presented against a background of various man-made influences on the aquatic ecosystems in this region. The State Fish Farm under study manages 56 lakes of total area over 5800 ha. For each of these lakes detailed records were available of the commercial catches of particular species and their artificial stockings over a period of 31 years. These, their trends and inter-relationships have been analyzed. Artificial stockings represented one of the best methods of counteracting adverse changes taking place in the fish stocks, with a simultaneous utilization of the productive potential of the lakes. Against this background, forecasts are made of the expected changes, and basic approaches to the proper management of the fish stocks are suggested.     

Molecular diagnostics of medically important bacterial infections

Infectious diseases are common diseases all over the world. A recent World Health Organization report indicated that infectious diseases are now the world's biggest killer of children and young adults. Infectious diseases in non-industrialized countries caused 45% in all and 63% of death in early childhood. In developed countries, the emergence of new, rare or already-forgotten infectious diseases, such as HIV/AIDS, Lyme disease and tuberculosis, has stimulated public interest and inspired commitments to surveillance and control. Recently, it is reported that infectious diseases are responsible for more than 17 million deaths worldwide each year, most of which are associated with bacterial infections. Hence, the control of infectious diseases control is still an important task in the world. The ability to control such bacterial infections is largely dependent on the ability to detect these aetiological agents in the clinical microbiology laboratory. Diagnostic medical bacteriology consists of two main components namely identification and typing. Molecular biology has the potential to revolutionise the way in which diagnostic tests are delivered in order to optimise care of the infected patient, whether they occur in hospital or in the community. Since the discovery of PCR in the late 1980s, there has been an enormous amount of research performed which has enabled the introduction of molecular tests to several areas of routine clinical microbiology. Molecular biology techniques continue to evolve rapidly, so it has been problematic for many laboratories to decide upon which test to introduce before that technology becomes outdated. However the vast majority of diagnostic clinical bacteriology laboratories do not currently employ any form of molecular diagnostics but the use such technology is becoming more widespread in both specialized regional laboratories as well as in national reference laboratories. Presently molecular biology offers a wide repertoire of techniques and permutations of these analytical tools, hence this article wishes to explore the application of these in the diagnostic laboratory setting.     

Basic problems of serological laboratory diagnosis

Serological laboratory diagnosis is inflicted with at least two kinds of basic problems. One type relates to the fact that the serological diagnosis of infectious diseases is double indirect: First, to diagnose an infectious disease, the identification of the microbial agent is sought that caused the disease. Second, to identify this infectious agent, the patient’s immune response to potential agents is measured. So, the serological test is neither measuring directly disease nor the cause of the disease, but the patient’s immune system. Another type of problem is based on the fact that each person’s immune system is very individual. The exact physicochemical properties of antibodies are unique for each clone of antibodies. The way an individual’s immune system sees an infectious agent depends not only on the genetic makeup of the person but also on the personal experience from former encounters with infectious agents. Both types of problems lead to complexities in selecting the appropriate test, in interpreting the results, and in standardizing serological tests. Therefore, a close collaboration of the laboratory with the clinic is mandatory to avoid erroneous conclusions from serological test results, which might lead to wrong decisions in patient care.     

Myxosporea: a new look at long-known parasites of fish

With the identification of Myxosporea as agents of swimbladder inflammation (SBI) in carp, and proliferative kidney disease (PKD) in salmonids, this group of over 1000 protistan species has been receiving renewed attention. Almost all species are parasites offish, and some can cause serious losses in commercial fish farms. Yet adequate control measures cannot be planned without clarification of basic features of the parasites' life cycles and modes of transmission. In this article, Jiri Lom reviews progress in understanding these biological puzzles.     

A program against bacterial bioterrorism: improved patient management and acquisition of new knowledge on infectious diseases

In 2002 it was decided to establish laboratory facilities in Denmark for diagnosing agents associated with bioterrorism in order to make an immediate appropriate response to the release of such agents possible. Molecular assays for detection of specific agents and molecular and proteomic techniques for identification of bacteria were introduced as part of the program. All assays and techniques were made accessible for use in diagnosing patients, even when an intentional release was not suspected. Medical expertise on different diseases was established at the department as an integrated part of the program. The analyses included PCR assays for specific bacteria, identification of isolated bacteria by DNA sequencing, detection and identification of bacteria in clinical sample material by universal bacterial PCR and DNA sequencing, and identification of bacteria by mass spectrometry. The established analyses formed a basis on which a series of further developments was built. In addition to reducing the time for obtaining diagnoses and improving the accuracy of diagnosis of individual infected patients, the analyses provided new knowledge on the frequency and distribution of some bacterial infections, including Q fever, tularemia, trench fever, brucellosis, and melioidosis. The implementation of an antibioterrorism program in a clinical diagnostic setting improved the diagnostic possibilities for patients in Denmark and provided new epidemiologic information. It also introduced a number of diagnostic assays for bacterial infections not associated with bioterrorism that are difficult to culture or identify.     

WESTERN EQUINE AND ST. LOUIS ENCEPHALITIS IN MAN,CALIFORNIA, 1945-1950

A large group of etiologic agents, some known and some unknown, produce in man a clinical syndrome now labeled “infectious encephalitis.”The separation, from this larger group, of single disease entities which cause similar clinical symptoms is possible, but calls for diagnostic acumen plus supporting laboratory evidence. Two etiologically specific entities, western equine encephalitis and St. Louis encephalitis, are frequently encountered in rather well-defined areas of California, the Central Valley and Imperial Valley; and there is a definite seasonal pattern of occurrence—June through October. There are certain guides that are helpful in differential diagnosis. Establishing a diagnosis on the basis of clinical evidence is difficult. Laboratory studies are of great importance not only for diagnosis in the individual case but for advancement of etiology. Specimens are worthless unless taken at proper intervals and submitted by methods described.It is probable that encephalitides caused by still unknown agents exist in California. The isolation and identification of new encephalitogenic viral agents will depend in large measure upon the submission by physicians of suitable specimens from patients with central nervous system disease in which the cause is obscure.     

Genetic Stock Identification of Chum Salmon in the Bering Sea and North Pacific Ocean Using Mitochondrial DNA Microarray

A newly developed DNA microarray was applied to identify mitochondrial (mt) DNA haplotypes of more than 2200 chum salmon in the Bering Sea and North Pacific Ocean in September 2002 and also 2003, when the majority of maturing fish were migrating toward their natal river. The distribution of haplotypes occurring in Asian and North American fish in the surveyed area was similar in the 2 years. A conditional maximum likelihood method for estimation of stock compositions indicated that the Japanese stocks were distributed mainly in the north central Bering Sea, whereas the Russian stocks were mainly in the western Bering Sea. The North American stocks were abundant in the North Pacific Ocean around the Aleutian Islands. These results indicate that the Asian and North American stocks of chum salmon are nonrandomly distributed in the Bering Sea and the North Pacific Ocean, and further the oligonuleotide DNA microarray developed by us has a high potential for identification of stocks among mixed ocean aggregates of high-seas chum salmon.     

Body pigmentation pattern to assess introgression by hatchery stocks in native Salmo trutta from Mediterranean streams

Five qualitative and seven quantitative colouration and spotting pattern features were measured in 23 brown trout Salmo trutta populations and two hatchery stocks. Simultaneously, the LDH‐C1 *, a diagnostic locus fixed for *90 and *100 alleles in stocking and native populations from southern Europe, respectively, was analysed to classify the brown trout studied according to their origin: native, hatchery stock and hybrids. The three genotypes showed significant differences in the colouration and spotting features and a discriminant function analysis could correctly identify 79% of the individuals. The most discriminating variables were dorsal fin margin colour, number of opercular spots, presence of the preopercular mark and diameter of black spots. Given the low cost, ease and possibility of field identification of native fish, the results indicate great opportunities for the application of morphological‐based classification models on the conservation and management of native brown trout stocks.     

Diagnostic approaches to Alzheimer's disease

The importance of obtaining an accurate and early diagnosis for Alzheimer's disease is now becoming recognized. Nonpharmacological as well as pharmacological therapies can be best initiated once a diagnosis is obtained. Biochemical markers to identify Alzheimer's disease have been sought for many years, with many candidates proposed. Recently criteria were established to evaluate putative diagnostic tests. Several biomarkers now show utility in identifying those with Alzheimer's disease. The ApoE e4 allele, while a risk factor rather than a deterministic gene, in the context of an individual with suspicion of AD has a positive predictive value of 94-98% and may come to have utility in predicting response to certain classes of pharmacological agents. Independent groups have shown that the markers in cerebrospinal fluid tau and Ab42 are, respectively, elevated and reduced in patients with AD versus other patient groups and that the lumbar puncture itself is usually well tolerated. For early-onset AD, sequencing presenilin 1 has come into use and the positive frequency is similar to that found in other genetic-based laboratory tests.     

Parasites of Cynoscion guatucupa along South American Atlantic coasts: evidence for stock discrimination

Two stocks of striped weakfish Cynoscion guatucupa in the south‐west Atlantic Ocean, were identified using parasites as biological tags. A total of 297 fish caught in Brazil, Uruguay and Argentina, contained 29 species of metazoan parasites. Univariate analysis on parasite populations, as well as multivariate discriminant analysis, calculated for juvenile and adult fish separately, allowed the identification of the two stocks, one from Argentina and Uruguay and the other from Brazil, to be made. Southern samples were characterized by higher prevalences and abundance of larval endohelminths, whereas in the northern stock, gastrointestinal and ectoparasitic species were common. Discriminant analyses on parasite infracommunities of Brazilian fish showed notable differences between juvenile and adult hosts; no such trend was observed in fish from Argentina and Uruguay, despite differences between juveniles and adults at the population level. Different oceanographic conditions and their influence on the distribution of parasites as well as of other hosts involved in their life cycles could be key factors for the differences observed among stocks of C. guatucupa .     

Antipodean aquaculture agents

Parallel features exist among diseases in Antipodean hosts when compared with those in other tropical and temperate regions. These features can be associated between infections in fish and prawns and between infections in freshwater and saltwater systems. Both fish and prawns are prone to physical stress, to behavioural stress, and to both introduced and native disease agents, agents that are limiting factors in several established aquaculture ventures. Both types of hosts are reared in a variety of facilities, each allowing for a different dynamic predisposition for disease. These diseases include those caused by native freshwater, estuarine and marine agents in both introduced and native hosts, and by introduced agents in those hosts. Some infections reflect unexpected or unidentifiable agents and host responses. Much can be learned in Australia and New Zealand from the infections, successes, failures and innovative methodologies experienced or used in the rest of the world. Potential in the Antipodes for production of unique and abundant fishery products is immense for both local and export markets. Approaches, however, should remain cautious regarding introductions and persistent regarding the investigation of potential diseases, host responses, diagnostic methods and management techniques.     

Merits and Pitfalls of Currently Used Diagnostic Tools in Mycetoma

Treatment of mycetoma depends on the causative organism and since many organisms, both actinomycetes (actinomycetoma) and fungi (eumycetoma), are capable of producing mycetoma, an accurate diagnosis is crucial. Currently, multiple diagnostic tools are used to determine the extent of infections and to identify the causative agents of mycetoma. These include various imaging, cytological, histopathological, serological, and culture techniques; phenotypic characterisation; and molecular diagnostics. In this review, we summarize these techniques and identify their merits and pitfalls in the identification of the causative agents of mycetoma and the extent of the disease. We also emphasize the fact that there is no ideal diagnostic tool available to identify the causative agents and that future research should focus on the development of new and reliable diagnostic tools.     

It is the economy,stupid! Projecting the fate of fish populations using ecological–economic modeling

Four marine fish species are among the most important on the world market: cod, salmon, tuna, and sea bass. While the supply of North American and European markets for two of these species – Atlantic salmon and European sea bass – mainly comes from fish farming, Atlantic cod and tunas are mainly caught from wild stocks. We address the question what will be the status of these wild stocks in the midterm future, in the year 2048, to be specific. Whereas the effects of climate change and ecological driving forces on fish stocks have already gained much attention, our prime interest is in studying the effects of changing economic drivers, as well as the impact of variable management effectiveness. Using a process‐based ecological–economic multispecies optimization model, we assess the future stock status under different scenarios of change. We simulate (i) technological progress in fishing, (ii) increasing demand for fish, and (iii) increasing supply of farmed fish, as well as the interplay of these driving forces under different scenarios of (limited) fishery management effectiveness. We find that economic change has a substantial effect on fish populations. Increasing aquaculture production can dampen the fishing pressure on wild stocks, but this effect is likely to be overwhelmed by increasing demand and technological progress, both increasing fishing pressure. The only solution to avoid collapse of the majority of stocks is institutional change to improve management effectiveness significantly above the current state. We conclude that full recognition of economic drivers of change will be needed to successfully develop an integrated ecosystem management and to sustain the wild fish stocks until 2048 and beyond.     

Numerical Diagnostic Key for the Identification of Enterobacteriaceae

A numerical diagnostic key for enteric organisms is described which permits the identification of typical strains and of biochemical variants with high accuracy. Unknown strains are inoculated into a basic set of five media which permit the testing of eight biochemical reactions. The positive reactions are assigned points, and the score of a strain is added up, after which the identification of the strain is obtained from a table. In many instances, the final identification is obtained with this set of biochemical tests; and, in other instances, a small number of additional tests are required to distinguish between organisms giving the same score in the basic set of biochemical tests. The key permits an accurate, rapid, and economical differentiation of the typical and the more common atypical biotypes of enteric organisms in the clinical laboratory.