Form and Function of Proteins. Historical Background and the Indian Effort in Macromolecular Crystallography

Global efforts in macromolecular crystallography started in the thirties of the last century. However, definitive results began to emerge only in the late fifties and the early sixties. India has a long tradition in crystallography. The country had a head start in theoretical and computational structural biology, thanks to the efforts of G.N. Ramachandran and his colleagues in the fifties and the sixties. However, macromolecular crystallography got off the ground in India only in the eighties, particularly after the Bangalore group received adequate support from the Department of Science and Technology under their Thrust Area Programme. The Bangalore centre was also identified as a national nucleus for the development of the area in the country. Since then work in the area has spread widely and is being carried out by several groups, mainly led by scientists trained at Bangalore or their descendents, in about thirty institutions in India. In addition to the Department of Science and Technology, the effort is now supported by other agencies like the Department of Biotechnology and the Council of Scientific and Industrial Research. The problems addressed by macromolecular crystallographers in India encompass almost all aspects of modern biology. Indian efforts in macromolecular crystallography have also become an important component of the international efforts in the area.

REDUCING COMPUTATIONAL EFFORT IN SOLVING GEOMECHANICS PROBLEMS WITH UPPER BOUND FINITE ELEMENTS LIMIT ANALYSIS AND LINEAR OPTIMIZATION

This paper presents a simple technique for reducing the computational effort while solving any geotechnical stability problem by using the upper bound finite element limit analysis and linear optimization. In the proposed method, the problem domain is discretized into a number of different regions in which a particular order (number of sides) of the polygon is chosen to linearize the Mohr-Coulomb yield criterion. A greater order of the polygon needs to be selected only in that region wherein the rate of the plastic strains becomes higher. The computational effort required to solve the problem with this implementation reduces considerably. By using the proposed method, the bearing capacity has been computed for smooth and rough strip footings and the results are found to be quite satisfactory.

Structural diversity and ligand specificity of lectins. The Bangalore effort

Structural studies in this laboratory encompass four of the five major classes of plant lectins, including the one discovered by us. In addition to addressing issues specific to individual lectins, the work provided insights into protein folding, quaternary association and generation of ligand specificity. Legume and beta-prism fold lectins constitute families of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary structure, including that involving an open structure. Strategies for generating ligand specificity include water bridges, variation in loop length, post translational modification and oligomerization. Three of the structural classes investigated have subunits with three-fold symmetry. The symmetry in the structure is reflected in the sequence to different extents in different subclasses. The evolutionary implications of this observation have been explored. The work on lectins has now been extended to those from mycobacteria.

Pulse vs. Optimal Stationary Fishing: The Northern Stock of Hake

Pulse fishing may be a global optimal strategy in multicohort fisheries. In this article we compare the pulse fishing solutions obtained by using global numerical methods with the analytical stationary optimal solution. This allows us to quantify the potential benefits associated with the use of periodic fishing in the Northern Stock of hake. Results show that: first, management plans based exclusively on traditional reference targets as Fmsy may drive fishery economic results far from the optimal; second, global optimal solutions would imply, in a cyclical manner, the closure of the fishery for some periods and third, second best stationary policies with stable employment only reduce optimal present value of discounted profit in a 2%.

Lessons from the northern hake long-term management plan: Could the economic assessment have accepted it?

An economic expert working group (STECF/SGBRE-07-05) was convened in 2007 for evaluating the potential economic consequences of a Long-Term Management Plan for the northern hake. Analyzing all the scenarios proposed by biological assessment, they found that keeping the F in the status quo level was the best policy in terms of net present values for both yield and profits. This result is counter intuitive because it may indicate that effort costs do no affect the economic reference points. However, it is well accepted that the inclusion of costs affects negatively the economic reference points. In this paper, applying a dynamic agestructured model to the northern hake, we show that the optimal fishing mortality that maximizes the net present value of profits is lower than Fmax.

Report of the Study Group on “Ecosystem-Based Management Science and its application to the North Pacific”

EXECUTIVE SUMMARY INTRODUCTION OVERVIEW OF INTERNATIONAL EBM HISTORY References CANADA Overview Activities to date Integrated Management implementation in Canada Objectives, indicators and reference points Assessment approaches Research directions for the future Management directions for the future References JAPAN Overview Conservation and sustainable use of marine living resources Harvest control by TAC system Stock Recovery Plan and effort regulation system Stock enhancement by hatchery-produced juvenile release Conservation and sustainable develop-ment on coastal waters The implementation of ecosystem-based management PEOPLE’S REPUBLIC OF CHINA Overview Current actions Output control Input control Summer fishing ban Enhance ecosystem health REPUBLIC OF KOREA Initiatives and actions of ecosystem-based management in Korea Current ecosystem-based management initiatives in Korea Precautionary TAC-based fishery management Closed fishing season/areas Fish size- and sex-controls Fishing gear design restrictions Marine protected areas (MPA) RUSSIA Existing and anticipated ecosystem-based management initiatives Issues related to the implementation of ecosystem-based management UNITED STATES OF AMERICA Definitions and approaches to ecosystem-based fishery management in the United States Present U.S. legislative mandates relating to ecosystem-based fishery management Target species Bycatch species Threatened or endangered species Habitats Food webs Ecosystems Integration of legislative mandates into an ecosystem approach Scientific issues in implementing ecosystem-based approaches References DISCUSSION AND RECOMMENDATIONS APPENDICES Appendix 10.1 Study group membership and participants Appendix 10.2 Terminology definitions Appendix 10.3 Present state of implementing ecosystem-based fishery management in Alaska: Alaska groundfish fisheries Appendix 10.4 Present state of implementing ecosystem-based fishery management off the West Coast of the United States: Pacific Coast groundfish fisheries Appendix 10.5 Descriptions of multi-species and ecosystem models developed or under development in the U.S. North Pacific region that might be used to predict effects of fishing on ecosystems Appendix 10.6 A potential standard reporting format (developed by Australia, and currently being used by the U.S.A in their contribution to this report) (83 page document)

Proposal for improving fishing opportunities off Pt. Loma by construction of an artificial reef

(Document pdf contains 42 pages)

ICSF guide book: understanding the Work in Fishing Convention, 2007

This guidebook attempts to provide a quick overview of the Work in Fishing Convention, 2007, which was adopted in Geneva, Switzerland, in June 2007 at the 96th International Labour Conference (ILC) of the International Labour Organization (ILO). It does not purport to provide interpretation of any provisions of the Convention and should not in any way be treated as a substitute for the actual provisions it contains. This guidebook is intended mainly to help those unfamiliar with the Convention and the working of the ILO and the ILC, gain some understanding of the relevant issues. In particular, it is hoped that the guidebook will aid fish workers and their organizations understand the possible benefits and implications of the Convention for artisanal and small-scale fisheries in developing countries.

Selectivity, pulse fishing and endogenous lifespan in Beverton-Holt models

Optimal management in a multi-cohort Beverton-Holt model with any number of age classes and imperfect selectivity is equivalent to finding the optimal fish lifespan by chosen fallow cycles. Optimal policy differs in two main ways from the optimal lifespan rule with perfect selectivity. First, weight gain is valued in terms of the whole population structure. Second, the cost of waiting is the interest rate adjusted for the increase in the pulse length. This point is especially relevant for assessing the role of selectivity. Imperfect selectivity reduces the optimal lifespan and the optimal pulse length. We illustrate our theoretical findings with a numerical example. Results obtained using global numerical methods select the optimal pulse length predicted by the optimal lifespan rule.

Tax-Based Fisheries Management: The Case Study Of The Cantabrian Anchovy Fishery

A dynamic optimisation framework is adopted to show how tax-based management systems theoretically correct the inefficient allocation of fishing resources derived from the stock externality. Optimal Pigouvian taxes on output (τ) and on inputs (γ) are calculated, compared and considered as potential alternatives to the current regulation of VIII division Cantabrian anchovy fishery. The sensibility analysis of optimal taxes illustrates an asymmetry between (τ) and (γ) when cost price ratio varies. The distributional effects also differ. Special attention will be paid to the real implementation of the tax-based systems in fisheries.

An examination of the Community Fisheries Sub-Decree in Cambodia: changes and developments during the drafting process

This study examines the development of the Community Fisheries Sub-Decree. From its promulgation in late 2000 through its draft form in June 20021, this sub-decree has gone through over 25 drafts. Initially, the writing process involved the public intimately: community meetings were conducted, NGOs contributed their knowledge and expertise, and then, with these consultations in mind, the newly-formed Community Fisheries Development Office (CFDO) in the Department of Fisheries (DoF) drafted the sub-decree. Over the following year and a half, the sub-decree went through numerous changes, some of which fundamentally alter the tenor of the legislation. This includes the deletion of some of the primary issues of rural communities, such as what fishing gears they can use and whether they can participate in patrolling the fishing area. While the final form is still pending, there are many questions as to the positive effects that the sub-decree will ultimately have on people’s livelihoods when it is finally approved. This research was undertaken to track the development of the sub-decree to gain a better understanding of how the Cambodian policy-making system functions. Consultations were undertaken with the DoF and CFDO before the research began, both of which agreed to the study. It is hoped that this report will help not only those interested in community fisheries issues, but also those who want to advocate on other Cambodian development issues as well. Due to the sensitive nature of the subject material, and the fact that the sub-decree is still pending, the author has conducted interviews with the express purpose of keeping them confidential. Therefore, no individual will be quoted directly in this study. In addition, many of the English versions of the drafts examined were unofficial translations. The author has made no effort to correct the English in the drafts. Moreover, there are also questions regarding the drafts and their sequence, as no government records were kept of the process or the changes that were made along the way. These have been compiled after the fact. (33 p.)