A review of the biology, ecology and management of Scirpus Olneyi. Volume 1: An annotated bibliography of selected references

This annotated bibliography of selected literature on Olney's three7square (Scirpus olneyi Gray )compiled basically for two reasons: 1) to assist a task force in its pursuit of an explanation for the substantial reduction in marsh acreage at the Blackwater National Wildlife Refuge in Dorchester County, Maryland, and 2) to serve as the author's foundation for the initiation of ecological research on this species as partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Botany Department of the University of Maryland. Both purposes are directly related in that the Author's research will be of use to the task force, along I with its other technical information and research results, in under-standing and possibly correcting the marshland loss problem at the Refuge. (PDF contains 100 pages)

Reproductive biology of Orechromis niloticus (L.) (Pisces: Cichlidae) in the Nyanza Gulf of Lake Victoria

Fish samples were collected using seine and trawl nets in Nyanza Gulf, Lake Victoria (Kenya) in order to study the reproductive and gonadal patterns of Oreochromis niloticus; samples were collected from June 1998 to February 1999. The variation in relative condition factor and monthly variation in gonad weight showed spawning took place between June and July. Most ripe fish were recovered between November and February, while a slight drop in GSI for males was noted between November and January. External factors triggering reproductive strategy are now being addressed

Single cell proteomics microchip to profile immune function, with applications in stem cell biology, translational disease mechanism study and clinical therapeutics monitoring

In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.

To study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor – killer immunoglobulin-like receptor (KIR) – has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.

In all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-α, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-α, IL-6 and GM-CSF. TLR stimulation activated the NF-κB signaling in HSCs. Single cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.

Biology of the mullet species occurring in the estuaries of Freetown Peninsula

This brief paper gives some notes on the geographical distribution and salinity tolerances of some Mugil species occurring in the Black-Johnson estuary, Sierra Leone

(Report of the) Institute of Marine Biology and Oceanography, Fourah Bay College, University of Sierra Leone

Details are given of the Institute and its activities, in particular the research projects being undertaken. These include studies on the marine molluscs of Sierra Leone, the cockle fishery, a preliminary investigation on the fouling organisms affecting the raft-cultured oyster populations, larval oyster ecology in relation to oyster culture, preliminary studies on the reproductive cycle of the mangrove oyster (Crassostrea tulipa), and catch composition of fishes taken by beach-seines at Lumley (Freetown). Records of the west African manatee (Trichechus senegalensis) are noted.

Contribution to the biology and geographical distribution of Aegagropila sauteri (Nees) Kutz. [Translation of: Gidrobiologicheskie Zhurnal, Kiev 4(3), 68-69, 1967]

Aegagropila sauteri is a peculiar green algae, the branched thalli of which, according to the amount of growth, forms velvety spheres of a diameter of 3-4, sometimes to 5-6 cm. and bigger. Investigators attribute it to a special genus of green algae. The authors examine Aegagropila sauteri in Lake Markakol (Kazakhstan).

Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.

Some observations on the temporal variations of size of copepods and some answers to questions on their biology. [Translation from: Internationale Revue der Gesamten Hydrobiologie und Hydrographie 17 99-114, 1927.]

Until now observations on the temporal variation of size of freshwater copepods have not provided much information. Other observers only mention in passing this or that phenomenon from which it is possible to deduct termporal variations. In this study Cyclops strenuus s.l., a freshwater species of fairly wide distribution, is studied in two water bodies. The author studies the systematic, placing of inhabitants described as C. strenuus Fischer in both locations, their annual life cycle, and their annual size variations.

Sensing and Actuation from Biology to Electronics

We introduce an in vitro diagnostic magnetic biosensing platform for immunoassay and nucleic acid detection. The platform has key characteristics for a point-of-use (POU) diagnostic: portability, low-power consumption, low cost, and multiplexing capability. As a demonstration of capabilities, we use this platform for the room temperature, amplification-free detection of a 31 bp DNA oligomer and interferon-gamma (a protein relevant for tuberculosis diagnosis). Reliable assay measurements down to 100 pM for the DNA and 1 pM for the protein are demonstrated. We introduce a novel "magnetic freezing" technique for baseline measurement elimination and to enable spatial multiplexing. We have created a general protocol for adapting integrated circuit (IC) sensors to any of hundreds of commercially available immunoassay kits and custom designed DNA sequences.

We also introduce a method for immunotherapy treatment of malignant gliomas. We utilize leukocytes internalized with immunostimulatory nanoparticle-oligonucleotide conjugates to localize and retain immune cells near the tumor site. As a proof-of-principle, we develop a novel cell imaging and incubation chamber for in vitro magnetic motility experiments. We use the apparatus to demonstrate the controlled movement of magnetically loaded THP-1 leukocytes.

Finally, we introduce an IC transmitter and power ampli er (PA) that utilizes electronic digital infrastructure, sensors, and actuators to self-heal and adapt to process, dynamic, and environmental variation. Traditional IC design has achieved incredible degrees of reliability by ensuring that billions of transistors on a single IC die are all simultaneously functional. Reliability becomes increasingly difficult as the size of a transistor shrinks. Self-healing can mitigate these variations.

Biology of the amphipod Gammarus pulex L. in water-bodies of the Leningrad district, and its piscicultural importance [Translation from: Trudy Vsesoyuznogo Gidrobiologicheskogo Obshchestva 7 99-122, 1956]

Observations and laboratory experiments are summarised that examine the widely discussed issue of what Gammarus pulex feeds on. On the basis of the observations of the authors and data from the literature it can be noted that G. pulex belongs to the omnivorous organisms, but, depending on the conditions of subsistence, in its rations either plant or animal food can predominate.

A study of the reproductive biology of dace in the middle Ob [introduction , summary and table captions only] [Translation from: Trudy tomsk. gos. Univ. 125, pp.77-91]

The Siberian Dace (Leuciscus leuciscus baicalensis (Dyb)is an important trade fish in Siberian waters. In the Ob basin more than 30,000 centners are produced annually. Catches of dace fluctuate significantly both between different rivers and between years in the Tomsk region. Defining the stocks of dace in the waters of the Tomsk region and explaining the fluctuations over time seems to be a very important and relevant question for the workers of the fishing industry. An answer, however, requires an accurate knowledge of the biology of dace; its reproductive, feeding and migration habits and the conditions of wintering etc. In the following we examine one of the above questions i.e. the biology of the reproduction of dace. The study was carried out in the Middle Ob in May 1951. This tranlations provides the introduction, summary and table captions only of the original article.

Changes in feeding biology of Nile tilapia, Oreochromis niloticus (L.), after invasion of water hyacinth, Eichhornia crassipes (Mart.) Solms, in Lake Victoria, Kenya

Oreochrimis niloticus (L.) was introduced to Lake victoria in the 1950s. It remained relatively uncommon in catches until 1965, when the numbers began to increase dramatically. It is now the third most important commercial fish species after the Nile perch, Lates niloticus (L.) and Rastrineobola argentea (Pellegrin). Oreochromis niloticus is considered a herbivore, feeding mostly on algae and plant material. The diet now appears to be more diversified , with insects, fish, algae and plant materials all being important food items. Fish smaller than 5 cm TL have a diverse diet but there is a decline in the importance of zooplankton, the preferred food item of small fish, as fish get larger. The shift in diet could be due to changes which have occurred in the lake. Water hyacinth, Eichhornia crassipes (Mart.) Solms, which harbours numerous insects in its root balls, now has extensively coverage over the lake. The native fish species which preyed on these insects (e.g. haplochromines) have largely been eliminated and O. niloticus could be filling niches previously occupied by these cichlids and non cichlid fishes. The change in diet could also be related to food availability and abundance where the fish is feeding on the most readily available food items.

Reproductive biology of Rastrineobola argentea (Pellegrin) in the northern waters of Lake Victoria

Size at first maturity, breeding periods and condition factor were determined for the small pelagic cyprinid Rastrineobola argentea (Pellegrin) in the Jinja waters of Lake Victoria in 1996-1997. Females showed a reduced size at maturity compared to ten years earlier when exploitation of the species was minimal. The males, however, have changed little. Although the species breeds throughout the year, two breeding peaks were observed during the drier months of August and December-January. Minimal breeding was observed in the rainy months of April-May and October-November. Fish from the open water station at Bugaia showed a higher proportion of breeding individuals than those from inshore areas. The mean monthly condition factor of fish from Napoleon Gulf confirmed breeding peaks obtained from examination of gonad development.

Reproductive biology of Oreochromis niloticus (L.) in the Nyanza Gulf of Lake Victoria

The reproduction of Nile tilapia, Oreochromis niloticus (L.), in the Nyanza Gulf of Lake Victoria was studied from June 1998 to May 1999. Length at maturity ranged from 28-30 cm TL for females and from 32-34 cm TL for males. Males were more abundant in all length classes longer than 36 cm TL. Relative condition factor was above unity, except in August, October and May for males, and October for females. Gonadosomatic index (GSI) was low during the post spawning period (July to October) and high during the protracted breeding period (December-June).

Aspects of the biology of coarse fish in the Dorset Stour

Some of the results from an investigation of five species of coarse fish, in the Stour River, carried out from 1968-1978 are presented in this article. The species involved were: Rutilus rutilis, Leuciscus leuciscus, L. cephalus, Esox lucius and Perca fluviatilis : which are of particular interest to anglers. Although these species show some similarities, as in the shape of the annual and seasonal growth curves, in most other respects each species occupies a distinct niche in the ecosystem and has a life-history strategy peculiar to itself. In this study only 5 species were investigated. When all the species present are considered the relationships or diversities suggested here will therefore be made far more complex.