Pollen selection — past,present and future

 A series of studies, recently reviewed, has established that approximately 60% of the structural genes which are expressed in the sporophytic portion of the angiosperm life cycle are also expressed and exposed to selection in the pollen. Given the haploidy and large population sizes of pollen grains, a substantial portion of the sporophytic genome could thus be periodically exposed to a bacterial type of mass screening. This extraordinary possibility is often subject to some skepticism which may, of course, be justified. However, recent attempts to apply models appear to be inappropriate in this context, in part because these attempts overlook an important source of genetic variation, and also because they assume fixed values for selection and fitness. More recently, studies of pollen/pollen interactions have suggested that what Linskens termed the ”programic phase” may represent an arena for important, and largely unexplored phenomena, some of which are discussed here. Received: 3 June 1996 / Revision accepted: 26 July 1996     

Plant mitochondria – past,present and future

The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10–600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000–3000 different proteins containing many unique proteins such as 200–300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.     

The β-lactam antibiotics: past, present, and future

The discovery and development of the -lactam antibiotics are among the most powerful and successful achievements of modern science and technology. Since Fleming's accidental discovery of the penicillin-producing mold, seventy years of steady progress has followed, and today the -lactam group of compounds are the most successful example of natural product application and chemotherapy. Following on the heels of penicillin production by Penicillium chrysogenum came the discoveries of cephalosporin formation by Cephalosporium acremonium, cephamycin, clavam and carbapenem production by actinomycetes, and monocyclic -lactam production by actinomycetes and unicellular bacteria. Each one of these groups has yielded medically-useful products and has contributed to the reduction of pain and suffering of people throughout the world. Research on the microbiology, biochemistry, genetics and chemistry of these compounds have continued up to the present with major contributions being made by both individual and collaborative groups from industry and academia. The discovery of penicillin not only led to the era of the wonder drugs but provided the most important antibiotics available to medicine. Continued efforts have resulted in the improvement of these compounds with respect to potency, breadth of spectrum, activity against resistant pathogens, stability and pharmacokinetic properties. On the research front, major advances are being made on structural and regulatory biosynthetic genes and metabolic engineering of the pathways involved. New semisynthetic compounds especially those designed to combat resistance development are being examined in the clinic, and unusual non-antibiotic activities of these compounds are being pursued. Although seventy years of age, the -lactams are not yet ready for retirement.     

The prokaryotic tree of life: past, present... and future?

No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.     

Phylogeography’s past,present, and future: 10 years after

Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of “likelihood-free” approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.     

The Paradigms They Are a-Changin’: past,present and future of PVC bacteria research

These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.     

TNF and TNF-receptors: From mediators of cell death and inflammation to therapeutic giants – past,present and future

Tumor Necrosis Factor (TNF), initially known for its tumor cytotoxicity, is a potent mediator of inflammation, as well as many normal physiological functions in homeostasis and health, and anti-microbial immunity. It also appears to have a central role in neurobiology, although this area of TNF biology is only recently emerging. Here, we review the basic biology of TNF and its normal effector functions, and discuss the advantages and disadvantages of therapeutic neutralization of TNF – now a commonplace practice in the treatment of a wide range of human inflammatory diseases. With over ten years of experience, and an emerging range of anti-TNF biologics now available, we also review their modes of action, which appear to be far more complex than had originally been anticipated. Finally, we highlight the current challenges for therapeutic intervention of TNF: (i) to discover and produce orally delivered small molecule TNF-inhibitors, (ii) to specifically target selected TNF producing cells or individual (diseased) tissue targets, and (iii) to pre-identify anti-TNF treatment responders. Although the future looks bright, the therapeutic modulation of TNF now moves into the era of personalized medicine with society's challenging expectations of durable treatment success and of achieving long-term disease remission.     

Shoreline displacement of Lake Ladoga — new data from Kilpolansaari

Dating of sediments sampled from small lakes in the Kilpolansaari region, in the NW part of Lake Ladoga, indicate that the River Neva, which is the present outlet of Lake Ladoga, originated at 3,100 radiocarbon years BP This is in agreement with some earlier estimations but no consensus concerning the age of the River Neva has previously been reached. New diatom data provide information concerning salinity and nutrient conditions in northern Lake Ladoga prior to the formation of the River Neva, when the Litorina Sea occupied the Baltic basin and approached the level of the ancient Lake Ladoga. Some slightly brackish water diatom species may indicate occasional saline water incursions into the Ladoga basin but, on the other hand, slightly brackish water species also occur in the present Lake Ladoga.     

Drugs from slugs—Past,present and future perspectives of ω-conotoxin research

Peptides from the venom of carnivorous cone shells have provided six decades of intense research, which has led to the discovery and development of novel analgesic peptide therapeutics. Our understanding of this unique natural marine resource is however somewhat limited. Given the past pharmacological record, future investigations into the toxinology of these highly venomous tropical marine snails will undoubtedly yield other highly selective ion channel inhibitors and modulators. With over a thousand conotoxin-derived sequences identified to date, those identified as ion channel inhibitors represent only a small fraction of the total. Here we discuss our present understanding of conotoxins, focusing on the ω-conotoxin peptide family, and illustrate how such a seemingly simple snail has yielded a highly effective clinical drug.     

Trends in staffing an academic department of surgery in a tropical hospital: past,present, and future?

OBJECTIVE--To evaluate the effect of staff mobility on student teaching, the training of young surgeons, and the volume of research in an academic department of surgery of a tropical teaching hospital. DESIGN--Retrospective study of academic staffing in the department of surgery of the Ahmadu Bello University Teaching Hospital between 1975 and 1993. SETTING--Zaria, Nigeria. SUBJECTS--42 academic staff, 1190 medical students, and 110 registrars (trainee surgeons). MAIN OUTCOME MEASURES--Number of academic staff in post, medical students, and registrars; number of research papers in latter years of the study. RESULTS--In 19 years, 42 academic staff worked for varying periods (1-15 years) in the university department of surgery in Zaria. These included six professors, 12 senior lecturers, and 24 lecturers. Although staff numbers diminished, numbers of students and registrars increased year by year. Average number of publications dropped from a peak of 14.4 to 7.4 a year. CONCLUSION--Staffing of the department has fallen steadily over the years and has adversely affected the department''s primary responsibility of teaching students and training young surgeons.     

Bacterial genomes in epidemiology—present and future

Sequence data are well established in the reconstruction of the phylogenetic and demographic scenarios that have given rise to outbreaks of viral pathogens. The application of similar methods to bacteria has been hindered in the main by the lack of high-resolution nucleotide sequence data from quality samples. Developing and already available genomic methods have greatly increased the amount of data that can be used to characterize an isolate and its relationship to others. However, differences in sequencing platforms and data analysis mean that these enhanced data come with a cost in terms of portability: results from one laboratory may not be directly comparable with those from another. Moreover, genomic data for many bacteria bear the mark of a history including extensive recombination, which has the potential to greatly confound phylogenetic and coalescent analyses. Here, we discuss the exacting requirements of genomic epidemiology, and means by which the distorting signal of recombination can be minimized to permit the leverage of growing datasets of genomic data from bacterial pathogens.