Weekend bioRxiv.org Preprint Review: Social inheritance can explain the structure of animal social networks

This week's bioRxiv preprint is an article about social networks in spotted hyena (Crocuta crocuta), rock hyrax (Procavia capensis), bottlenose dolphin (Tursiops spp), and sleepy lizard (Tiliqua rugosa). The article uses a model of social network formation where a newborn forms attachment most to its mother (probability = pb), second most likely to its mother's social contacts (probability pn), and then less likely to those of its species not already networked to its mother (probability pr). These are species where it is observed that fathers do not generally participate in childrearing.

They found that a computer model where pb > pn > pr models observed relationships in these societies better than other models considered. Note that such relationships are an example of an emergent behavior, and perhaps can be seen as supporting an emergent culture, though to be sure that this is cultural it would noted that it is likely that in such societies that there would be a mirrored DNA relatedness that would confound such a conclusion, as detailed and accounted for in Whitehead and Rendell's book we reviewed last year.




Social inheritance can explain the structure of animal social networks

Amiyaal Ilany and Erol Akcay

bioRxiv preprint first posted online Sep. 4, 2015; doi: http://dx.doi.org/10.1101/026120.

The social network structure of animal populations has major implications for survival, reproductive success, sexual selection, and pathogen transmission of individuals. But as of yet, no general theory of social network structure exists that can explain the diversity of social networks observed in nature, and serve as a null model for detecting species and population-specific factors. Here we propose a simple and generally applicable model of social network structure. We consider the emergence of network structure as a result of social inheritance, in which newborns are likely to bond with maternal contacts, and via forming bonds randomly. We compare model output to data from several species, showing that it can generate networks with properties such as those observed in real social systems. Our model demonstrates that important observed properties of social networks, including heritability of network position or assortative associations, can be understood as consequences of social inheritance.

Weekend bioRxiv.org Preprint Review: Cortical rhythms are modulated by respiration

As most runners who check their pulse know, the pulse rate is strongly influenced by the breathing rate. What is more interesting from a neuroscience perspective is that EEG patterns, including the cortical gamma oscillations, are strongly influenced by respiration as well.

In the paper below, Heck and colleagues report that in both experimental mice subjects and in human subjects undergoing EEG monitoring with implanted electrodes, the EEG gamma activity shows a strong tie in its power to the phases of respiration.

Their findings go a long way to explain the increase in gamma band reported during meditation. Persons experienced with traditional deep meditation techniques often show a marked slowing of breathing rates with meditation, and it seems that it is in that space between inspirations that Heack et al report the rise in gamma power to occur, in both mouse and man.

For me, this paper resonates with some of my memories of residency and fellowship work in Denver in the nineteen-eighties. Dr. James Austin, one of my neurology professors from those years in Colorado, is widely published regarding his neurological interest in Zen meditation. He wrote as far back as 1999 a book, a copy of which sits on my office bookshelf, which discusses from a philosophical and medical perspective the neurological changes which occur in Zen monks during meditation.

Why does this EEG gamma power modulation with respiration occur, and what might be its links to limbic or cognitive functions? Is the change in gamma mediated by a vagal tone influence, as likely explains the changes in heart rate with respiration, or is it via another, perhaps hypothalamic pathway? This remains to be seen.


Cortical rhythms are modulated by respiration

Detlef H. Heck, Samuel S. McAfee, Yu Liu, Abbas Babajani-Feremi, Roozbeh Rezaie, Walter J. Freeman, James W. Wheless, Andrew C. Papanicolaou, Miklós Ruszinkó, Robert Kozma

bioRxiv preprint first posted online Apr. 16, 2016; doi: http://dx.doi.org/10.1101/049007.


The brain generates oscillatory neuronal activity at a broad range of frequencies and the presence and amplitude of certain oscillations at specific times and in specific brain regions are highly correlated with states of arousal, sleep, and with a wide range of cognitive processes. The neuronal mechanisms underlying the generation of brain rhythms are poorly understood, particularly for low-frequency oscillations. We recently reported that respiration-locked olfactory bulb activity causes delta band (0.5-4 Hz) oscillatory neuronal activity in the whisker sensory (barrel) cortex in mice. Furthermore, gamma oscillations (30 – 100Hz), which are widely implicated in cognitive processing, were power-modulated in synchrony with the respiratory rhythm. These findings link afferent sensory activity caused by respiration directly to cortical rhythms associated with cognitive functions. Here we review the related literature and present new evidence to propose that respiration has a direct influence on oscillatory cortical activity, including gamma oscillations, and on transitions between synchronous and asynchronous cortical network states (marked by phase transitions). Oscillatory cortical activity, as well as phase transitions, has been implicated in cognitive functions, potentially linking respiratory phase to cognitive processing. We further argue that respiratory influence on cortical activity is present in most, and possibly in all areas of the neocortex in mice and humans. We furthermore suggest that respiration had a role in modulating cortical rhythms from early mammalian evolution. Early mammals relied strongly on their olfactory sense and had proportionately large olfactory bulbs. We propose that to this day the respiratory rhythm remains an integral element of dynamic cortical activity in mammals. We argue that breathing modulates all cortical functions, including cognitive and emotional processes, which could elucidate the well-documented but largely unexplained effects of respiratory exercises on mood and cognitive function.

A tree of life, 2016.

All of pre-microscope biology fits upon a single leaf of the newest tree. Megafauna may be big in size, but not in numbers of species, compared to the massive numbers of non-eukaryocytic species.


What works best for jellyfish stings?

Perhaps an exposure suit, rinsed well after climbing out of the sea, prevents them the best :-)

According to UH Manoa professor Angel Yanagihara, vinegar is the best readily available household liquid to pour on the tentacles, to prevent cubozoan jellyfish tentacle sting firing (otherwise, brushing the jellyfish tentacle off causes more stings). Prior folk wisdom to the contrary, alcohol and urine are not nearly as good, and hot water is better than cold.

Guided by the new jellyfish sting assay described in the article below, the group is now marketing a proprietary, copper and magnesium ion-based spray-on formulation that the abstract below says works even better than vinegar. At least a plastic bottle of vinegar, or perhaps Sting-No-More, belongs in the scuba first aid kit, for those occasional jellyfish envenomations.


Experimental Assays to Assess the Efficacy of Vinegar and Other Topical First-Aid Approaches on Cubozoan (Alatina alata) Tentacle Firing and Venom Toxicity

Angel A. Yanagihara, Christie Wilcox, Rebecca King, Kikiana Hurwitz, and Ann M. Castelfranco

Received: 30 October 2015 / Accepted: 4 January 2016 / Published: 11 January 2016

Abstract: Despite the medical urgency presented by cubozoan envenomations, ineffective and contradictory first-aid management recommendations persist. A critical barrier to progress has been the lack of readily available and reproducible envenomation assays that (1) recapitulate live-tentacle stings; (2) allow quantitation and imaging of cnidae discharge; (3) allow primary quantitation of venom toxicity; and (4) employ rigorous controls. We report the implementation of an integrated array of three experimental approaches designed to meet the above-stated criteria. Mechanistically overlapping, yet distinct, the three approaches comprised (1) direct application of test solutions on live tentacles (termed tentacle solution assay, or TSA) with single image- and video-microscopy; (2) spontaneous stinging assay using freshly excised tentacles overlaid on substrate of live human red blood cells suspended in agarose (tentacle blood agarose assays, or TBAA); and (3) a “skin” covered adaptation of TBAA (tentacle skin blood agarose assay, or TSBAA). We report the use and results of these assays to evaluate the efficacy of topical first-aid approaches to inhibit tentacle firing and venom activity. TSA results included the potent stimulation of massive cnidae discharge by alcohols but only moderate induction by urine, freshwater, and “cola” (carbonated soft drink). Although vinegar, the 40-year field standard of first aid for the removal of adherent tentacles, completely inhibited cnidae firing in TSA and TSBAA ex vivo models, the most striking inhibition of both tentacle firing and subsequent venom-induced hemolysis was observed using newly-developed proprietary formulations (Sting No More™) containing copper gluconate, magnesium sulfate, and urea.

Citrus grafting results at four weeks

Sanboukan sweet lemon citrus tree grafts after a month, unwrapped today. The first graft looks more solidly healed than the second. We will see how the buds grow.

New Feature: Weekend bioRxiv.org Preprint Review

Cold Spring Harbor is now hosting bioRxiv.org, a preprint archive of biology papers, similar to the well known, decades-old physics one at at Cornell's arXiv.org. This archive, if it becomes generally used, should break the unfair paywalls on publicly funded study results, at least for preprints. It should also allow often unpublishable negative studies to be placed where meta-analysts can use them. Therefore, this new archive deserves praise.

I intend to take advantage of this new source, and plan to review at least one preprint per weekend on this blog, unless the weekend gets too hectic. I intend to focus on neuroscience and clinical medicine related papers, but potentially will include other biological topics if they strike me as unusually interesting. Today, I'll review the only clinical trial paper in the archive so far.


A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors

Cinnamon S Bloss, Nathan E Wineinger, Melissa Peters, Debra L Boeldt, Lauren Ariniello, Ju Young Kim, Judy Sheard, Ravi Komatireddy, Paddy Barrett, Eric J Topol

bioRxiv doi: http://dx.doi.org/10.1101/029983


Background. Mobile health and digital medicine technologies are becoming increasingly used by individuals with common, chronic diseases to monitor their health. Numerous devices, sensors, and apps are available to patients and consumers -- some of which have been shown to lead to improved health management and health outcomes. However, no randomized controlled trials have been conducted which examine health care costs, and most have failed to provide study participants with a truly comprehensive monitoring system.

Methods. We conducted a prospective randomized controlled trial of adults who had submitted a 2012 health insurance claim associated with hypertension, diabetes, and/or cardiac arrhythmia. The intervention involved receipt of one or more mobile devices that corresponded to their condition(s) and an iPhone with linked tracking applications for a period of 6 months; the control group received a standard disease management program. Moreover, intervention study participants received access to an online health management system which provided participants detailed device tracking information over the course of the study. This was a monitoring system designed by leveraging collaborations with device manufacturers, a connected health leader, health care provider, and employee wellness program -- making it both unique and inclusive. We hypothesized that health resource utilization with respect to health insurance claims may be influenced by the monitoring intervention. We also examined health-self management.

Results & Conclusions. There was little evidence of differences in health care costs or utilization as a result of the intervention. Furthermore, we found evidence that the control and intervention groups were equivalent with respect to most health care utilization outcomes. This result suggests there are not large short-term increases or decreases in health care costs or utilization associated with monitoring chronic health conditions using mobile health or digital medicine technologies. Among secondary outcomes there was some evidence of improvement in health self-management which was characterized by a decrease in the propensity to view health status as due to chance factors in the intervention group.

Clinical trial registration ID # NCT01975428


The study was done on persons in the San Diego region who had hypertension, diabetes, or chronic cardiac arrhythmia. The subjects were given an iPhone based monitor for their condition which allowed them to periodically take a relevant measure of their condition and maintain records of these measurements with the Health Circles iPhone app. Both these persons and the controls were also "enrolled in the HealthComp disease management program, which involved outreach by HealthComp nursing staff for purposes of relaying medical education and wellness information with regard to disease prevention and chronic disease management."

The results were negative regarding health care financial costs: there was no endpoint statistical difference on health claims or visits to the hospital in the intervention group versus the control group.

This study suggests that adding a smartphone app database to the monitoring of chronic health conditions does not improve at least some measures of health costs. However, it does not include the newer, continuous monitoring devices, like the smartwatches which monitor pulse. I think that, to make a real difference in behavior, the measurement tech may need to function as a monitor in the background which can provide potentially unexpected feedback in the foreground when needed: it should be continuous and provide feedback otherwise not available to the patient, with little or no extra effort required by the patient. That type of technology is not yet available or ready for general use.

DNA studies show that female adultery is rarer in humans than previously thought.

So human women are better mates than are female songbirds? Who would have thought? :-).


Neuronal cell death: Apoptosis and Parthanatos

With ischemic stroke, portions of brain undergo cellular death with swelling, termed apoptosis, which causes characteristic changes on imaging studies. On the other hand, degenerative diseases such as Parkinson's cause cellular loss without apoptosis or swelling. This is termed parthanatos, because it is dependent on the Poly Adp-Ribose pathway.

The study below of a model for this type of neuronal cell loss might be used to test agents to prevent such neuronal cell death, hopefully with more success than past studies targeting apoptosis.



Cultured networks of excitatory projection neurons and inhibitory interneurons for studying human cortical neurotoxicity

Jin-Chong Xu, Jing Fan, Xueqing Wang, Stephen M. Eacker, Tae-In Kam, Li Chen, Xiling Yin, Juehua Zhu, Zhikai Chi, Haisong Jiang, Rong Chen, Ted M. Dawson, and Valina L. Dawson

Science Translational Medicine 06 Apr 2016:

Vol. 8, Issue 333, pp. 333ra48, DOI: 10.1126/scitranslmed.aad0623

Translating neuroprotective treatments from discovery in cell and animal models to the clinic has proven challenging. To reduce the gap between basic studies of neurotoxicity and neuroprotection and clinically relevant therapies, we developed a human cortical neuron culture system from human embryonic stem cells or human inducible pluripotent stem cells that generated both excitatory and inhibitory neuronal networks resembling the composition of the human cortex. This methodology used timed administration of retinoic acid to FOXG1+ neural precursor cells leading to differentiation of neuronal populations representative of the six cortical layers with both excitatory and inhibitory neuronal networks that were functional and homeostatically stable. In human cortical neuronal cultures, excitotoxicity or ischemia due to oxygen and glucose deprivation led to cell death that was dependent on N-methyl-D-aspartate (NMDA) receptors, nitric oxide (NO), and poly(ADP-ribose) polymerase (PARP) (a cell death pathway called parthanatos that is distinct from apoptosis, necroptosis, and other forms of cell death). Neuronal cell death was attenuated by PARP inhibitors that are currently in clinical trials for cancer treatment. This culture system provides a new platform for the study of human cortical neurotoxicity and suggests that PARP inhibitors may be useful for ameliorating excitotoxic and ischemic cell death in human neurons.

Congratulations to local town 2016 group women's hula winners, Halau O Ka Ua Kani Lehua!

I'm happy that a halau (hula dance studio) only six blocks from the stadium, a local favorite run by local great Johnny Lum Ho, got rewarded for a fabulous performance at the Merrie Monarch hula festival this past week. Congrats also to the men's group Halau Na Mamo o Pu‘uanahula, from Sonny Ching's big Honolulu school. They shone in all categories and took the overall title.

Congratulations to Miss Aloha Hula 2016

The winner this year was Kayli Kaiulani Carr, with her traditional performance in the hula video here.

I really liked the Wood Rose hula by a runner-up for the award, Kayshlyn Keauliʻimailani Victoria De Sa, with costume here:

So what is this flowery plant about which the hula is written? Actually, there are two Hawaiian wood roses! One is a kind of morning glory known for its ergoloid-containing seed, the baby woodrose:

... and one imported invasive vine, the Pilikai vine, Merremia tuberosa:
... and I believe the imported, rather invasive one is the one referred to in the hula.

I've been fighting this invasive wood rose vine for the past four years in one corner of our lot: once established, it continually re-sprouts when cut or pulled, from small tubers it makes underground from its deep roots. The dang thing can grow almost a foot in a single day. That vine does have very attractive yellow flowers, and the dried, flowery seed pods make nice leis or necklaces, but it can smother a small tree in just weeks. So though the hula was beautiful, its theme might not have resonated completely, I think.

On the reports of human CRISPR research.

What He Jiankui et al., 2018 said was an important ethical principle. What He Jiankui claims he did by usi...