The Cell and Protoplasm as Container,Object, and Substance, 1835–1861

This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form. Second, I argue that in the 1840s, ideas of what formless, biological matter was capable of dramatically changed: going from a “coagulation paradigm” (Pickstone, 1973) that had existed since Theophrastus, to a more robust conception of matter that was itself capable of movement and self-maintenance. In addition to revisiting Schleiden and Schwann’s original writings on cell theory, this article looks especially closely at Hugo von Mohl’s definition of the protoplasm concept in 1846, how it differed from his primordial utricle theory of cell structure two years earlier. This article draws on Lakoff and Johnson’s theory of “ontological metaphors” to show that the cell, primordial utricle, and protoplasm can be understood as material container, object, and substance, and that these overlapping distinctions help explain the chaotic and confusing early history of cell theory.     

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 Fly Agaric,Soma,Father Christmas and the Vikings

1　ThemushroomTheFlyAgaric (Amanitamuscaria (L :Fr.)Hooker)belongstothegenusAmanitaPers .,agroupwhichhasplayedmajorrolesinhumanaffairsthrough outhistory .Itincludesboththemostlydeadlypoi sonousspeciesandpossiblythemostdeliciousspeciesofalloftheediblewildmushrooms.TheFlyAgaricrepresentsthebestknownofallthewildmushroomsandhadthegreatesteffectuponmankindandworldhistory .Itistobeseeninmanychildren′sbooksasthelarge ,brightredmushroomwiththewhitespots,invariablyassociatedwithfairiesandelves.It…     

The phylogeny and evolution of thePterygodium—Corycium complex (Coryciinae,Orchidaceae)

The leaf-anatomy, palynology, seed-morphology, vegetative morphology and especially the highly complicated floral morphology of theCoryciinae s. str. (Diseae: Orchidoideae: Orchidaceae) are described and illustrated in detail. On the basis of these characters the presumed phylogeny, based on a rigorous cladistic analysis, is presented. The cladistic biogeographical analysis of theCoryciinae s. str. shows that it is a member of the Afrotemperate Track, with a pattern of vicariance events typical of the members of this track. An analysis of the patterns of speciation shows that allopatric speciation appears to be rare, and that parapatric speciation across edaphic boundaries may be the most important factor. Proceeding from the information presented, a new classification of the group is proposed in which we recognize the four generaCeratandra, Evotella, Pterygodium andCorycium. The new monotypic genusEvotella comprises a species originally described asPterygodium rubiginosum. The three species of the genusAnochilus are transferred toCorycium andPterygodium. P. magnum, which was originally described asPterygodium but was transferred toCorycium lately, is placed in a monotypic section ofPterygodium.     

The ‘Antiretrovirals,Sexual Transmission Risk and Attitudes’ (ASTRA) Study. Design,Methods and Participant Characteristics

Life expectancy for people diagnosed with HIV has improved dramatically however the number of new infections in the UK remains high. Understanding patterns of sexual behaviour among people living with diagnosed HIV, and the factors associated with having condom-less sex, is important for informing HIV prevention strategies and clinical care. In addition, in view of the current interest in a policy of early antiretroviral treatment (ART) for all people diagnosed with HIV in the UK, it is of particular importance to assess whether ART use is associated with increased levels of condom-less sex. In this context the ASTRA study was designed to investigate current sexual activity, and attitudes to HIV transmission risk, in a large unselected sample of HIV-infected patients under care in the UK. The study also gathered background information on demographic, socio-economic, lifestyle and disease-related characteristics, and physical and psychological symptoms, in order to identify other key factors impacting on HIV patients and the behaviours which underpin transmission. In this paper we describe the study rationale, design, methods, response rate and the demographic characteristics of the participants. People diagnosed with HIV infection attending 8 UK HIV out-patient clinics in 2011-2012 were invited to participate in the study. Those who agreed to participate completed a confidential, self-administered pen-and-paper questionnaire, and their latest CD4 count and viral load test results were recorded. During the study period, 5112 eligible patients were invited to take part in the study and 3258 completed questionnaires were obtained, representing a response rate of 64% of eligible patients. The study includes 2248 men who have sex with men (MSM), 373 heterosexual men and 637 women. Future results from ASTRA will be a key resource for understanding HIV transmission within the UK, targeting prevention efforts, and informing clinical care of individuals living with HIV.     

The Tiotropium Safety and Performance in Respimat? Trial (TIOSPIR?), a large scale,randomized, controlled,parallel-group trial-design and rationale

Background

Tiotropium bromide is an effective therapy for COPD patients. Comparing across programs tiotropium Respimat® Soft Mist™ inhaler was at least as efficacious as tiotropium HandiHaler®, however, concerns have been raised about tiotropium’s safety when given via Respimat®.

Methods

The TIOSPIR® trial ({"type":"clinical-trial","attrs":{"text":"NCT01126437","term_id":"NCT01126437"}}NCT01126437) compares the safety and efficacy of tiotropium Respimat® 5 μg once daily (marketed) and 2.5 μg once daily (investigational) with tiotropium HandiHaler® 18 μ once daily (marketed). The hypotheses to be tested are 1). that tiotropium Respimat® 5 μg once daily and Respimat® 2.5 μg once daily are non-inferior to HandiHaler® in terms of all-cause mortality, and 2). that tiotropium Respimat® 5 μg once daily is superior to HandiHaler® in terms of time to first exacerbation. A spirometry substudy evaluates the bronchodilator efficacy. The trial is a randomized, double-blind, double dummy, event-driven, parallel group study. Participants can use any background treatment for COPD except inhaled anticholinergic agents. The study encompasses a wide range of COPD patients, e.g. patients with stable cardiac diseases including arrhythmia can be included. Clinical sites are international and include both primary care as well as specialists.

Results

To date, over 17,000 participants have been randomized from over 1200 sites in 50 countries with an anticipated treatment duration of 2–3 years.

Conclusion

TIOSPIR® will provide precise estimates of the relative safety and efficacy of the Respimat® and HandiHaler® formulations of tiotropium, assess potential dose-dependence of important outcomes and provide information on the clinical epidemiology of COPD in a large international patient cohort.     

The Human Cystathionine β-Synthase (CBS) Gene: Complete Sequence, Alternative Splicing, and Polymorphisms

Cystathionine β-synthase [CBS; -serine hydro-lyase (adding homocysteine), EC 4.2.1.22] catalyzes the first committed step of transsulfuration and is the enzyme deficient in classical homocystinuria. In this report, we describe the molecular cloning and the complete nucleotide sequence of the human CBS gene. We report a total of 28,046 nucleotides of sequence, which, in addition to the CBS gene, contains 5 kb of the 5′ flanking region. The human CBS gene contains 23 exons ranging from 42 to 209 bp. The 5′ UTR is formed by 1 of 5 alternatively used exons and 1 invariably present exon, while the 3′ UTR is encoded by exons 16 and 17. We also describe the identification of two alternatively used promoter regions that are GC rich (80%) and contain numerous putative binding sites for Sp1, Ap1, Ap2, and c-myb, but lack the classical TATA box. The CBS locus contains an unusually high number ofAlurepeats, which may predispose this gene to deleterious rearrangements. Additionally, we report on a number of DNA sequence repeats that are polymorphic in North American and European Caucasians.     

Fixed,free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian–Triassic origin

Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian–Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid diversity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231–252 mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian–Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon sampling are needed to recover a more robust phylogeny of the group.     

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction,Dedifferentiation, and Diabetes

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The HIV epidemic in China： history, response, and challenge

The first case of AIDS was reported in 1985 in China, but by the early 21st century, the government estimated that there were 840,000 citizens living with HIV/AIDS. The number is increasing rapidly. The major risk groups are injection drug users （IDUSs; 43%） and former plasma donors （27%）, but rates among heterosexual groups are rising rapidly. Sentinel surveillance was initiated in 1986, and now includes IDUs, men-who-have-sex-with-men, sexually transmitted disease clinic attendees, antenatal women, long-distance truck drivers, and sex workers. Although the government was slow to respond to the epidemic in the late 20th century, it has made a vigorous response in the early 21st century. Components of that response include implementation and evaluation of harm reduction programs for IDUs, education to increase knowledge and reduce stigma, treatment and social support for rural and poor HIV/AIDS patients, widespread testing, and increased funding for HIV/AIDS programs. International agencies have been generous in their support of the government initiatives. To successfully combat the epidemic, China needs to develop and train the necessary infrastructure to implement its intervention programs, particularly in the rural areas, to vigorously combat stigma and discrimination, support research especially in the universities and research institutions other than the China Centers for Disease Control, develop a system for efficient exchange of research and program information, and update legislation to reflect the current situation.     

The Bainbridgia — Dualipora association (Cnidaria,Tabulata): palaeogeographical and palaeoecological implications

The genera Bainbridgia and Dualipora (Cnidaria, Tabulata) have been found together in 4 localities of Early Devonian age (Missouri, USA; Tafilalt, Morocco; Barrandian, Czechoslovakia; Hörre, Germany). Several isolated occurrences of each are also reported. The palaeogeographical and palaeoecological implications of this association are discussed.     

The Chemical Syntheses of (2′-5′)-P-Thioadenylate Dimers,Trimers and Tetramers

Abstract

The dimeric, trimeric and tetrameric 2′-5′-adenylate phosphothioates were synthesized via the phosphoramidite method using the p-nitrophenylethyl (NPE) group for phosphate protection and followed by sulfur oxidation. The various diastereoisomers were separated by chromatographical means and characterizes in their structures.     

The Sun,Moon, Wind,and Biological Imperative–Shaping Contrasting Wintertime Migration and Foraging Strategies of Adult Male and Female Northern Fur Seals (Callorhinus ursinus)

Adult male and female northern fur seals (Callorhinus ursinus) are sexually segregated in different regions of the North Pacific Ocean and Bering Sea during their winter migration. Explanations for this involve interplay between physiology, predator-prey dynamics, and ecosystem characteristics, however possible mechanisms lack empirical support. To investigate factors influencing the winter ecology of both sexes, we deployed five satellite-linked conductivity, temperature, and depth data loggers on adult males, and six satellite-linked depth data loggers and four satellite transmitters on adult females from St. Paul Island (Bering Sea, Alaska, USA) in October 2009. Males and females migrated to different regions of the North Pacific Ocean: males wintered in the Bering Sea and northern North Pacific Ocean, while females migrated to the Gulf of Alaska and California Current. Horizontal and vertical movement behaviors of both sexes were influenced by wind speed, season, light (sun and moon), and the ecosystem they occupied, although the expression of the behaviors differed between sexes. Male dive depths were aligned with the depth of the mixed layer during daylight periods and we suspect this was the case for females upon their arrival to the California Current. We suggest that females, because of their smaller size and physiological limitations, must avoid severe winters typical of the northern North Pacific Ocean and Bering Sea and migrate long distances to areas of more benign environmental conditions and where prey is shallower and more accessible. In contrast, males can better tolerate often extreme winter ocean conditions and exploit prey at depth because of their greater size and physiological capabilities. We believe these contrasting winter behaviors 1) are a consequence of evolutionary selection for large size in males, important to the acquisition and defense of territories against rivals during the breeding season, and 2) ease environmental/physiological constraints imposed on smaller females.     

The summer flounder chronicles: Science,politics, and litigation, 1975–2000

The summer flounder, or fluke (Paralichthys dentatus)supports the most important commercial and recreational flatfishfisheries of the U.S. Atlantic coast. Thestock and fishery range from Massachusetts toNorth Carolina. Spawning takes place during aprotracted season that can extend fromSeptember to March, during an annual offshoreand southern migration to the outer continentalshelf off Virginia and North Carolina. Thefish are con-centrated in bays and estuariesfrom late spring through early autumn, when thenext offshore migration begins. The assessmentand management of the summer flounder fisheryhas been very contentious since theimplementation of the joint Atlantic StatesMarine Fisheries Commission/Mid-AtlanticFishery Management Council Fishery ManagementPlan (FMP) in 1989, when the poor status of thesummer flounder stock was evident toscientists, managers, and fishermen. Amendment2 to the FMP, approved in 1992, implementedseveral major regulatory provisions includingannual commercial quotas and recreationalharvest limits, and annually adjustable minimumlanded fish sizes, minimum mesh sizes,possession limits, and seasonal closures. By1999, fishing mortality on summer flounder haddeclined to its lowest level since the 1960s,and summer flounder total stock biomass was thehighest since the mid-1970s. Monitoring ofstock status is ongoing to reliably determine``how much fish is enough' to provide forlong-term sustainability. Many changes are madeannually to management measures due todiffering interpretations of stock status bymanagers, and fishery and environmentaladvocacy groups. Attainment of the annualfishing mortality targets remains elusive. Themultiple layers of science, management, andpolitics in place since 1992 continue to sparkmuch controversy and litigation that increasingly places the management of the summer flounder fishery in the hands of the courts.