Reply to comments by R. Osczevski on “Modified wind chill temperatures determined by a whole body thermoregulation model and human-based convective coefficients” by Ben Shabat,Shitzer, and Fiala (2013) and “Facial convective heat exchange coefficients in cold and windy environments estimated from human experiments” by Ben Shabat and Shitzer (2012)

This article is a reply to comments by R. Osczevski on “Modified wind chill temperatures determined by a whole body thermoregulation model and human-based convective coefficients.”     

Highly regioselective hydrolysis of tricarballylates (“retro-fats”) and citrates by subtilisin

Trimethyl and triethyl esters of tricarballylic acid and citric acid were hydrolysed with porcine liver esterase(PLE) to the isomeric diesters. In all cases the hydrolysis took place with poor regioselectivity (maximum 50% excess). However, the hydrolysis of trimethyl and triethyl esters of tricarballylic acid and of the triethyl ester of citric acid with subtilisin was absolutely regioselective and the symmetric 1,5-diester was obtained.     

Harassment and killing of porpoises (“phocoenacide”) by fish-eating Southern Resident killer whales (Orcinus orca)

Endangered Southern Resident killer whales (Orcinus orca) are fish-eaters that preferentially prey on adult Chinook salmon (Oncorhynchus tshawytscha). Despite being salmon specialists, individuals from all three killer whale pods (J, K, L) have been observed harassing and killing porpoises (family Phocoenidae) without consuming them. Retrospectively, we identified and analyzed 78 episodes of Southern Resident killer whales harassing porpoises between 1962 and 2020, of which 28 resulted in the porpoise's death (“phocoenacide”). Fifty-six episodes involved harbor porpoise (Phocoena phocoena), 13 involved Dall's porpoise (Phocoenoides dalli), and the porpoise species was unreported for nine episodes. Southern Resident killer whales often targeted young porpoises that were similar in size to adult Chinook salmon. Both sexes participated in porpoise harassment. Juveniles engaged in the behavior the most; however, their rates of engagement were not found to differ significantly from most other age classes. The behavior was passed through generations and social groupings, as it was first observed in L pod and spread to the other two pods. Killer whales are highly complex animals known to exhibit social learning and cultural transmission of learned behaviors, but the reason(s) for this behavior is unknown. Hypotheses include the social and developmental benefits of play, hunting practice, or displaced epimeletic behavior.     

DEPTOR ubiquitination and destruction by SCF(β-TrCP)

β-Transducin repeats-containing protein (β-TrCP) is the substrate recognition subunit of the SCF (SKP1, CUL1, and F-box protein)-type E3 ubiquitin ligase complex. SCF(β-TrCP) ubiquitinates specifically phosphorylated substrates to promote their subsequent destruction by the 26S proteasome and plays a critical role in various human diseases including tumorigenesis. We and others (Duan S et al. Mol Cell 44: 317-324, 2011; Gao D et al. Mol Cell 44: 290-303, 2011; Zhao Y et al. Mol Cell 44: 304-316, 2011) recently reported that SCF(β-TrCP) regulates cell growth and autophagy by controlling the ubiquitination and destruction of DEPTOR, an endogenous mammalian target of rapamycin inhibitor, in a phosphorylation-dependent manner. In this review, we discuss β-TrCP's new downstream substrate, DEPTOR, as well as summarize the novel functional aspects of β-TrCP in controlling cell growth and regulating autophagy, in part through governing the stability of DEPTOR.     

Current chemical concepts of acids and bases and their application to anionic (“acid”) and cationic (“basic”) dyes

Summary In biomedical studies, dyes are divided into acid and basic dyes. This classification cannot be reconciled with current chemical definitions of acids and bases. Brönsted-Lowry acids are compounds that can donate protons; bases are proton acceptors. The definition of acids and bases is independent of the electric charge, i.e. acids and bases can be neutral, anionic or cationic. Reactions between acids and bases result in formation of new acid-base pairs. Lewis acids and bases do not depend on a particular element, but are characterized by their electronic configurations. Lewis bases are electron donors; Lewis acids are electron acceptors. This classification is also unrelated to the electric charge. Lewis acids and bases interact by formation of coordinate covalent bonds.In histochemistry and histology, dyes containing SO ₃ ^– , –COO^– and/or –O^– groups are classified as acid dyes. However, such compounds are electron pair donors and hence Brönsted-Lowry and Lewis anionic bases. Dyes carrying a positive charge are termed basic dyes. Chemically, many cationic dyes are Lewis acids because they can add a base, e.g. OH^–, acetate, halides. The hypothesis that transformation of –NH₂ into ammonium groups imparts basic properties to dyes is untenable; ammonium groups are proton donors and hence acids. Furthermore, conversion of an amino into an ammonium group blocks a lone electron pair and the color of the dye changes drastically, e.g. from violet to green and yellow. It appears therefore highly unlikely that ammonium groups are responsible for binding of cationic (basic) dyes. In histochemistry, it is usually not of critical importance whether anionic or cationic dyes are chemically acids or bases. It is therefore suggested to substitute the terms anionic for acid and cationic for basic dyes; this nomenclature will always be chemically correct.     

Nonspecific (“pseudo-plasmal”) dye-binding in the Feulgen nuclear stain and its blocking by azocarmin G

Summary In Feulgen nuclear staining nonspecific dye-binding due to the pseudo-plasmal reaction is intensified in isolated cells with intact cytoplasm, and cannot be eliminated by the post-irradiation method. Fluorescence intensity in the cytoplasm sometimes exceeds that of specific nuclear fluorescence, especially in brain and heart muscle cells, and it was almost impossible to perform cytofluorometric DNA quantification on such specimens. Various kinds of aldehyde-blocking agents such as sodium borohydride, 2,4-dinitrophenylhydrazine, aniline, and sodium pyrosulfite were effective in reducing the pseudo-plasmal reaction. But the blocking effects were not complete because of additional release of reactive aldehyde groups during subsequent Feulgen hydrolysis. Acidic azocarmin G produces a complete block of all pseudo-plasmal reaction in acriflavine-Feulgen nuclear staining, allowing accurate DNA-cytofluorometry to be carried out.     

Introduction to “Moral (and Other) Laboratories”

“Moral (and other) laboratories” is a special issue that draws on Cheryl Mattingly’s notion of the “moral laboratory” to explore the uncanny interface between laboratory ethnography and moral anthropology, and to examine the relationship between experience and experiment. We ask whether laboratory work may provoke new insights about experimental practices in other social spaces such as homes, clinics, and neighborhoods, and conversely, whether the study of morality may provoke new insights about laboratory practices as they unfold in the day-to-day interactions between test tubes, animals, apparatuses, scientists, and technicians. The papers in this collection examine issues unique to authors’ individual projects, but as a whole, they share a common theme: moral experimentation—the work of finding different ways of relating—occurs in relation to the suffering of something or someone, or in response to some kind of moral predicament that tests cultural and historically shaped “human values.” The collection as a whole intends to push for the theoretical status of not merely experience itself, but also of possibility, in exploring uncertain border zones of various kinds—between the human and the animal, between codified ethical rules and ordinary ethics, and between “real” and metaphorical laboratories.     

Comparison Between poly(dG-dC)·poly(dG-dC) and DNA Modified by cis-diamminedichloroplatinum (II): Immunological and Spectroscopic Studies

Abstract

The importance of the base composition and of the conformation of nucleic acids in the reaction with the drug cis-diamminedichloroplatinum(II) has been studied by competition experiments between the drug and several double-stranded polydeoxyribonucleotides. Binding to poly(dG)·poly(dC) is larger than to poly (dG-dC)·poly(dG-dC). There is no preferential binding in the competition between poly(dG-dC) ·poly(dG-dC), poly(dA-dC) ·poly(dG-dT) and poly(dA-dG)·poly(dC-dT). In the competition between poly(dG-dC) ·poly (dG-dC) (B conformation) and poly(dG-br⁵dC) ·poly(dG-br⁵dC) (Z conformation), the drug binds equally well to both polynucleotides. In natural DNA, modification of guanine residues in (GC)_n·(GC)_nsequences by the drug has been revealed by the inhibition of cleavage of these sequences by the restriction enzyme BssHII. By means of antibodies to platinated poly(dG-dC), it is shown that some of the adducts formed in platinated poly(dG-dC) are also formed in platinated pBR322 DNA. The type of adducts recognized by the antibodies is not known. Thin layer chromatography of the products after chemical and enzymatic hydrolysis of platinated poly(dG-dC) suggests that interstrand cross-links are formed. Finally, the conformations of poly(dG-m⁵dC) modified either by cis-diamminedichloroplatinum(II) or by trans-diammine- dichloroplatinum(II) have been compared by circular dichroism. Both the cis-isomer and the trans-isomer stabilize the Z conformation when they bind to poly(dG-m⁵dC) in the Z conformation. When they bind to poly(dG-m⁵dC) in the B conformation, the conformations of poly(dG-m⁵dC) modified by the cis or the trans-isomer are different. Moreover, the cis-isomer facilitates the B form-Z form transition of the unplatinated regions while the trans-isomer makes it more difficult.     

“Ixoroid” secondary pollen presentation and pollination by small moths in the Malagasy treeletIxora platythyrsa (Rubiaceae)

The pollination biology ofIxora platythyrsa (Rubiaceae) was studied in NW. Madagascar. The plant displayed cream-yellow, nocturnally fragrant, nectariferous, tubular and strongly protandrous flowers. These had an ixoroid secondary pollen presentation mechanism: prior to anthesis, anthers exhausted their pollen onto unripe stylar heads. From this position pollen of male-stage flowers later adhered to primarily the probosces of small visiting nocturnal noctuid and geometrid moths. — Pollen was subsequently raked off moths' probosces by receptive, copiously papillose stigmas of female-stage flowers. Principal pollination adaptation was probably to the noctuid moth subfam.Sarrothripinae.     

Is polecat (Mustela putorius) diet affected by “mediterraneity”?

Carnivores in Mediterranean ecosystems respond to the inherent heterogeneity of these systems by tracking the spatial and temporal availability of food resources. This feeding strategy, however, has been associated primarily with generalist carnivores and little is known for specialist species such as the European polecat. We collected polecat scat to determine the diet of this species, how it matches the seasonal availability of food resources, and how it is affected by population spatial structure and anthropogenic disturbance. Polecats were present in only 34% of the surveyed area and were clumped into three main population nuclei. Despite the spatial segregation of the populations, they had no significant differences in food items consumed. Polecats mostly fed on mammals (percentage of occurrence (P.O.)=43%) and arthropods (P.O.=49%). Biomass intake was also mostly from mammals (percentage of biomass (P.B.)=96%), followed by birds (P.B.=3%), with arthropods contributing less than 1%. Lagomorphs were the most consumed prey (P.O.=25% and P.B.=87%), which is consistent with the marked spatial overlap between scat with high content in lagomorphs and the areas with high wild rabbit availability. These results indicate that polecats are specialists in the consumption of wild rabbits, spatially track the availability of this prey, and may be affected by the decrease in abundance of the prey populations. Future conservation of polecats in Mediterranean regions of southern Portugal may be achieved through the restoration of hunted and diseased wild rabbit populations.     

Cardiac and neuroprotection regulated by α(1)-adrenergic receptor subtypes

Sympathetic nervous system regulation by the α(1)-adrenergic receptor (AR) subtypes (α(1A), α(1B), α(1D)) is complex, whereby chronic activity can be either detrimental or protective for both heart and brain function. This review will summarize the evidence that this dual regulation can be mediated through the different α(1)-AR subtypes in the context of cardiac hypertrophy, heart failure, apoptosis, ischemic preconditioning, neurogenesis, locomotion, neurodegeneration, cognition, neuroplasticity, depression, anxiety, epilepsy, and mental illness.     

Comparative Studies of Wild-Type and “Cold-Mutant” (Temperature-Sensitive) Influenza Viruses: Polypeptide Synthesis by an Asian (H2N2) Strain and Its Cold-Adapted Variant

The structure and replication of a cold-adapted, temperature-sensitive (TS) mutant of an Asian (H2N2) influenza virus was compared with that of its wild-type (WT) parent. Viruses were grown in a chicken kidney cell system, and at the nonpermissive temperature of 40 C, production of infectious TS virus was about 100,000-fold less than at 35 C, in contrast to WT virus. Major structural polypeptides of each virus grown at 35 C were similar, except that the hemagglutinin glycopolypeptide (HA) of the TS virions was slightly more heterogenous than that of WT virions. Synthesis of viral polypeptides was examined by sodium dodecyl sulfate acrylamide gel electrophoresis of pulse-labeled infected cells. This revealed a defect in the synthesis of TS viral hemagglutinin that was most pronounced at the nonpermissive temperature. Other TS viral polypeptides appeared to be synthesized normally at 40 C. A defect in the TS virus hemagglutinin was also indicated by serological studies that demonstrated that TS virus hemagglutinin had lost antigenic sites present on the WT virus. Thus, it is concluded that the virus mutant examined contains lesions in the hemagglutinin gene, although the possibility of additional unrecognized lesions is not excluded.     

Factor-free (“Non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes

Systems of poly(U)-directed polyphenylalanino synthesis by Escherichia coli ribosomes in the absence of elongation factors and GTP (factor-free system) or in the presence of one of the elongation factors and GTP (EF-G² and EF-T_u-deperident systems) are described. It is shown that the use of oligouridylates of different length as templates in the factor-free system results in peptides, the degree of polymerization of which does not exceed the number of template codons, i.e. a conjugated translocation of the peptidyl-tRNA and the template takes place. Thus, the function of translocation as well as the specific binding of aminoacyl-tRNA and transpeptidation proved to be intrinsic to the ribosome itself. The study of kinetics of polyphenylalanine synthesis and dependence of the synthesis rate on the Mg²⁺ concentration in the factor-free, EF-T_u-dependent and EF-G-dependent translation systems has demonstrated that the elongation factors with GTP promote ribosomal mechanisms of aminoacyl-tRNA binding and translocation, respectively. It turned out that the factor-free translation system does not display miscoding. It is the promotion of translocation by EF-G with GTP that has been found to be responsible in full measure for miscoding, while EF-T_U with GTP does not contribute to this.     

Reader reaction to “Outcome-adaptive lasso: Variable selection for causal inference” by Shortreed and Ertefaie (2017)

Shortreed and Ertefaie introduced a clever propensity score variable selection approach for estimating average causal effects, namely, the outcome adaptive lasso (OAL). OAL aims to select desirable covariates, confounders, and predictors of outcome, to build an unbiased and statistically efficient propensity score estimator. Due to its design, a potential limitation of OAL is how it handles the collinearity problem, which is often encountered in high-dimensional data. As seen in Shortreed and Ertefaie, OAL's performance degraded with increased correlation between covariates. In this note, we propose the generalized OAL (GOAL) that combines the strengths of the adaptively weighted L₁ penalty and the elastic net to better handle the selection of correlated covariates. Two different versions of GOAL, which differ in their procedure (algorithm), are proposed. We compared OAL and GOAL in simulation scenarios that mimic those examined by Shortreed and Ertefaie. Although all approaches performed equivalently with independent covariates, we found that both GOAL versions were more performant than OAL in low and high dimensions with correlated covariates.     

Calcium transport by rabbit skeletal muscle microsomes (“fragmented sarcoplasmic reticulum”)

Ca²⁺ binding by skeletal muscle microsomes in 5 mM ATP exhibited saturation kinetics in the range of Ca²⁺ concentrations between 3 · 10^?8 and 10^?5 M. Approximately 140 nmoles binding sites per mg protein were found. These had a Ca²⁺ binding constant of approximately 4.5 · 10⁶ M^?1 with half saturation at 2.2 · 10^?7 M Ca²⁺. In the presence of oxalate, much larger amounts of Ca²⁺ (approx. 6 μmoles/mg protein) were taken up by the microsomes (Ca²⁺ uptake), but the rate of Ca²⁺ uptake increased linearly with [Ca²⁺] when ionized Ca²⁺ concentrations were below 3 · 10^?6 M. At Ca²⁺ concentrations above 3 · 10^?6, Ca²⁺ uptake was inhibited. Double reciprocal plots of the Ca²⁺ dependence of the initial rates of Ca²⁺ uptake in the concentration range between 3 · 10^?7 M and 10^?5 M, unlike those of Ca²⁺ binding, did not demonstrate saturation kinetics, but could be interpreted as representing a non-saturable system with inhibition at higher Ca²⁺ concentrations. In view of these differences, and because Ca²⁺-binding sites were almost fully saturated at 10^?6 M Ca²⁺, whereas Ca²⁺ uptake rate increased linearly with increasing [Ca²⁺] to approximately 3 · 10^?6 M, the Ca²⁺-binding sites are not shown kinetically to participate in oxalate-dependent Ca²⁺ uptake.     

“Cancer Nanotechnology: Methods and Protocols (Methods in Molecular Biology)” by Stephen R. Grobmyer (Editor), Brij M. Moudgil (Editor)

Cancer remains one of the leading causes of death. Research and resulting technologies have contributed to rising numbers of cancer survivors. Cancer nanotechnology is a novel and burgeoning field with the promise to open the door for the development of improved cancer therapies and detection methods. Cancer nanotechnology has the potential to become clinical reality.