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Posted in | Optics and Photonics | Photovoltaics and Solar Cells
High Precision Mirrors Forming Key Components in World's Largest Solar Telescope
From Optical Surfaces Ltd.May 27 2008
Optical Surfaces Ltd. has announced that it has delivered, to the Big Bear Solar Observatory (BBSO) located in Big Bear Lake, California, three high precision off-axis parabolic mirrors that will form key focusing components in the adaptive optical system associated with BBSO's new 1.6 metre solar telescope.
Due for completion later in 2008, the new 1.6 m aperture off-axis Gregorian solar telescope (http://www.bbso.njit.edu/) will be the world's largest telescope enabling precise studies of the physics of the Sun and observation of solar phenomena. The new BBSO solar telescope (NST) benefits from adaptive optics, which will allow atmospheric seeing to be corrected to the diffraction limit, an advanced computer systems capable of supporting sophisticated instruments such as Fabry-Perot interferometers and improved observation at infrared wavelengths. The adaptive optics will allow the BBSO NST to image actual photospheric flux tubes, at about 100 km resolution.
Commenting on their choice of supplier - Nicolas Gorceix (BBSO optical designer) stated ' Optical Surfaces Ltd. was selected to produce the critical focusing mirrors for the adaptive optics due to its technical excellence, reasonable pricing and a proven record in supplying ultra-smooth optics to leading astronomical research groups around the world.
Using proprietary production techniques, Optical Surfaces Ltd skilled craftsmen were able to produce the required three ultra-smooth 150mm diameter parabolic mirrors with a surface accuracy of lambda/10 p-v and excellent surface quality of 20:10 scratch / dig. All mirrors, effective focal length (2000mm), were given a protected silver coating offering peak performance from 0.39 - 1.6 microns.
Optical Surfaces Ltd has been producing optical components and systems for more than 45 years and is now accepted as one of Europe's leading manufacturers of high-precision optics for astronomical research. The company's main workshops and test facilities are deep underground in a series of tunnels excavated in solid chalk where temperature remains constant and vibration is practically non-existent. With such stable conditions testing particularly with long path lengths become quantifiable and reliable. Working with these natural advantages is a highly skilled team of craftsmen with a commitment to excellence in both product quality and customer service.
Optical Surfaces ISO 9001-2000 approved manufacturing facility provides the flexible resources to supply from single specialist requirements to OEM quantities. All high precision optics is provided with a complete quality test assurance report.
For further information on ultra smooth off-axis mirrors for astronomical telescopes please contact Optical Surfaces Ltd. by telephone on +44-208-668-6126 or email [email protected]
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Last Edit: 2014/06/11 21:46 By sleekpony.


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Rubber Biosynthesis in Plants
The Authors: Katrina Cornish and Joshua J. Blakeslee
Home Chemistry/Physics
Natural rubber is a strategically essential raw material throughout the world; global consumption is nearly 11 million metric tons each year, and demand is rapidly increasing. The United States is currently totally dependent upon the import of more than 1.2 million metric tons of natural rubber (NR) per year from tropically grown sources. The economic importance of maintaining a steady supply of NR is highlighted by the fact that the United States rubber products trade is worth over $18 billion annually, with a deficit growing to 72% in October 2010 (US Department of Commerce data). For more than a century, Hevea brasiliensis, or the para rubber tree, has provided almost all of the world's natural rubber, from a plantation and smallholding system involving tapping latex by hand. Most NR is produced in Southeast Asia, with <10% from Africa and ~1% from South America. Natural rubber prices reached all-time highs in 2011, primarily due to dramatically increased demand from both China and India. The independent International Rubber Study Group projects a 1.5 to 3 million metric ton shortfall in NR production by 2021. If the means to increase natural rubber production are not developed to meet rising NR demands, consumers worldwide will face a steep escalation in prices for products incorporating this material. While many nations are currently financing enormous expenditures to protect and develop both oil and mineral interests, it is surprising that means of augmenting the production of natural rubber, a vital strategic resource, are not being pursued.
The current market shortfall of NR is exacerbated by increasing petroleum costs driving up prices in the synthetic rubber industry, which is facing a shortage of butadiene, the monomer from which 80% of synthetic rubber is produced. Taken together, these issues prevent the natural and synthetic rubber markets from compensating for each other's high prices and/or production shortfalls, which they have historically been able to do. Furthermore, the genetic base of H. brasiliensis is extremely narrow, and vast acreages are planted as genetically identical clones, making the plantations prone to crop failure. South American Leaf Blight (SALB), the most deadly known H. brasiliensis disease caused by Microcyclus ulei, destroyed the South American rubber industry in the early twentieth century, with the result that very little rubber is produced in Brazil up to the present date. More recently, this devastating fungal pathogen has appeared in both India and Thailand and threatens the irreplaceable and economically vital populations of H. brasiliensis in these nations. Should SALB escape control measures, the current production of natural rubber in Southeast Asia could collapse with little or no advance warning.
The de facto selection of a single species to produce a globally important material has to date been largely a matter of chance and convenience. Natural rubber production is not limited to H. brasiliensis, however, and NR is produced by at least 2,500 plant species in four of the six major superorders of the dicotyledonous plants, as well as some fungi (Lactarius sp.). The distribution of rubber biosynthesis in the plant kingdom indicates that the ability to produce rubber evolved 100-200 million years ago, before or as the early dicotyledonous Angiosperms diverged from each other. Although all NR-producing species localize rubber production in the cytosolic component, individual species exhibit many differences in the details of their rubber biosynthesis, accumulation and compartmentalization.
Natural rubber, chemically, is a cis-1,4-polyisoprene polymer composed from isopentyl pyrophosphate monomers; usually with a C15 trans tail derived from the original initiating allylic pyrophosphate (a specific type of diphosphate). Natural rubber is an end product of one branch of the ubiquitous plant isoprenoid/terpenoid synthesis pathway. NR product quality is related, on the molecular level, to the polymer molecular weight, branching, gel content (insoluble, cross-linked rubber), and to the composition of the nonrubber components of the latex, and, on the cellular level, to the rubber particles in which the rubber polymers are compartmentalized. Species-specific differences in these parameters may be exploited using biotechnological approaches to produce different types of rubber, which may open up new product applications. Several other species are in commercial development, most notably Parthenium argentatum (guayule) and Taraxacum kok-saghyz (rubber, or Russian, dandelion), but Helianthius annuus, Chrysothamnus nauseosus, Cryptostegia grandifora, Solidago sp., Lactiflua sp. or Euphorbia lactiflua latex?, Ficus sp. and Euphorbia sp. and others have received focused attention.
Role of Rubber in Plants
In individual species, rubber-containing latex may play a role in disease resistance, wound healing or tolerance to environmental stress. Certainly, the cold-induction of rubber biosynthesis in P. argentatum is well established, as is the presence of antifungal and coagulant proteins in H. brasiliensis. However, remarkably, there is no unifying physiological role identified for rubber in plants. One possibility that has been raised is that rubber, an end product, serves, in part, to help condition plants to survive deleterious external stimuli. For example, rubber is produced in cold temperatures in temperate species like T. kok-saghyz and P. argentatum, and may play an important role in wound responses in tropical species such as H. brasiliensis and F. elastica. Additionally, in P. argentatum and H. brasiliensis (and possibly in other laticiferous species), no isoprene synthases are present to provide a means of respiring excess photosynthate (although larger volatile compounds are made) and rubber may serve as an excess assimilate sink to prevent damage to the photosynthetic apparatus under conditions of cold temperature and high light.
Rubber Particles
While relatively little is known about the physiological role of rubber synthesis in plant growth and development, the rubber biosynthetic particles (RPs), where the rubber polymerization reactions actually occur, have been more extensively studied. Rubber biosynthetic rate and polymer size are primarily regulated by the laticifers (Fig. 1), long multinucleate synciciate pipes formed from anatomized cells, in latex-producing species like H. brasiliensis, Ficus elastica, and T. kok-saghyz.
Figure 1. Transmission electronmicrograph of a rubber-containing laticifer (d'Auzac et al., 1989)
In nonlatex plants, such as P. argentatum, which produces rubber in bark parenchyma cells (Fig. 2) and transfers the mature rubber particles into the vacuole for storage, the regulation of rate and molecular weight has largely devolved to the rubber transferase enzyme itself. While studies to date have provided information on the size, composition, and synthetic capacity of developed, functional rubber particles, relatively little is known about the ontogeny, assembly and growth of RPs.
Figure 2. Scanning electron micrograph of bark parenchyma cells of stems of two-year old Parthenium argentatum, showing vacuoles filled with rubber particles (photograph by Delilah Wood, USDA).
The rubber transferase protein, or protein complex, is embedded in a unilamellar biological membrane surrounding a rubber core, with new rubber molecules being synthesized from hydrophilic pyrophosphate substrates and elongated into the hydrophobic particle. The composition of the rubber particle monolayer membrane is species-specific, consisting of structural phospholipids and sterols, as well as a collection of proteins unique to each species (with very low sequence identity) (Fig. 3). The presence of glycosylated proteins in the rubber particle membrane suggests an origin in the rough endoplasmic reticulum and passage through the Golgi vesicular trafficking network, but this has yet to be proven. While phospholipid, sterol, and fatty acid (FA) compositions vary between H. brasiliensis, F. elastica, and T. kok-saghyz, all rubber particle membranes examined contain significant amounts of phosphatidic acid, which functions as both a structural phospholipid and a lipid signaling molecule.
Figure 3. SDA-PAGE gel of rubber particle associated proteins in different species (Dr. Wenshuang Xie).
As might be expected given the divergent protein profiles present in rubber particles from different species, many of the proteins present in these organelles do not share common three-dimensional structures. This lack of a conserved immune response-inducing epitope across RPs derived from varying species is why guayule latex products can be safely used by people with Type I latex allergic reactions induced by proteins present in H. brasiliensis-derived latex.
The properties of rubber produced in RPs are also impacted by the nonprotein membrane components present, which are highly species-specific. H. brasiliensis particles contain an unusual furanoid FA, whereas those from F. elastica contain very long chain FAs (Table 1).
Table 1. Fatty acid compositions of the combined neutral, phospho- and glycolipids in rubber particles.
Species 16:0 18:0 18:1 18:2 18:3 20:0 22:0 24:0 26:0 28:0 Furanoid
Hevea 4 10 4 11 71
Guayule 9 2 8 53 28
Ficus 10 16 4 21 18 13 18
These F. elastica FAs, combined with the integral membrane proteins present in RPs in this species, lead to a stiff membrane, rather than the more common fluid membrane (Fig. 4).
Figure 4. Scanning electron micrographs of purified rubber particles (photograph by Delilah Wood, USDA).
Rubber particles from different species all contain rubber cores, but not all rubber-producing species make high molecular weight rubber (Fig. 5). Helianthus annuus (sunflower), for example, makes mostly low molecular weight rubber. Molecular weight, however, is a prime determinant of rubber quality, with high quality being correlated high molecular weight. Also, not all rubber forms gel - the spontaneous cross-linking of insoluble polymer within the rubber particles - which can hamper processing. Gel does not seem to be related to the amount of protein per particle or the polymer molecular weight. Guayule makes high molecular weight polymer but with no gel content at all.
Figure 5. Size exclusion chromatograms of rubber purified from several species (Dr. Colleen McMahan)
Biochemical Regulation of Rubber Yield and Molecular Weight
Rubber biosynthesis is catalyzed by a membrane-bound cis-prenyl transferase, rubber transferase (EC 2.5.1.20), found at the surface of cytoplasmic rubber particles. Active rubber transferase has not been purified, reproducibly, to date, and so biochemical investigations have relied on using purified, enzymatically active rubber particles, from which all cytoplasmic components have been removed. This appears to be a valid approach because kinetic analysis indicates that only one isopentenyl pyrophosphate (IPP)-using enzyme is present when rubber is synthesized, which must be the rubber transferase. Thus, purified rubber particles present a single enzyme system, positioned on a suitable aqueous-organic interface, valid for biochemical investigation. Further, the study of biochemical parameters on the native particles is likely to provide kinetic information directly applicable to the in vivo situation, something always questionable in the study of solubilized membrane-bound enzymes.
Rubber transferases are a class of cis-prenyl transferases (CPTs) with substrate binding constants distinct from other soluble and membrane-bound CPTs and are able to synthesize varying molecular weight cis-1,4-polyisoprene, including above 1 million g/mole (Fig. 5).
Biochemical studies demonstrate that the regulation of biosynthetic rate (a direct component of yield), and mature rubber molecular weight (a prime component of rubber quality), are largely controlled by the concentration of initiator (an allylic pyrophosphate, the C15 trans-farnesyl pyrophosphate in vivo, although many allylic pyrophosphates of different size and stereochemistry are effective in vitro), monomer (the nonallylic, C5, isopentenyl pyrophosphate) and activator (divalent cation, magnesium in vivo, while manganese also is effective in vitro). The polymerization reaction catalyzed by rubber transferase is a condensation reaction, which releases a pyrophosphate and a proton, and specifically occurs via an alkylation by prenyl transfer to the initiating allylic pyrophosphate (APP) - electrophile – by the monomer isopentenyl pyrophosphate (IPP) – nucleophile. Thus, elongating rubber molecules are allylic pyrophosphates. Interestingly, different rubber-producing species have also evolved additional fine control mechanisms, and some rubber transferase enzymes are able to at least partially regulate the molecular weight of mature rubber polymers.
In vivo, rubber biosynthesis is limited by the supply of allylic pyrophosphate initiator, but even more so by the supply of IPP monomer. Recently, genetic transformation systems have been developed and engineered to "metabolically funnel" carbon into rubber production by both increasing the supply of IPP and initiating the synthesis of substrates that only rubber transferase can use. These systems are working well in P. argentatum and in T. kok-saghyz.
Extensive biochemical investigation of rubber biosynthesis in Hevea brasiliensis, Parthenium argentatum (guayule), Taraxacum kok-saghyz and Ficus sp. has demonstrated that plant species synthesize rubber in essentially the same way and their rubber transferases have similar characteristics – indeterminate product size, high KmIPP, high metal [A]max, metal cofactor requirements, and integral membrane localization. Further, in all species the concentration and reaction of monomer and initiator affect the biosynthetic rate, the number of rubber molecules synthesized and the molecular weight of the polymers produced. However, the divergent anatomical evolution in the above species has resulted in the co-evolution of several interesting differences in their respective rubber transferases, allowing all three to maintain rubber synthesis in their unique ecological niche. For example, P. argentatum (guayule) rubber transferase has a much wider range of negative cooperativity for the initiator farnesyl pyrophosphate (FPP) (Fig. 6) than is seen in the corresponding H. brasiliensis or F. elastica enzymes. In other words, when one FPP binds to the active site of guayule rubber transferase, the next FPP is unable to compete the first one off again to start a new rubber molecule. This, combined with the remarkably small KmFPP in this species, allows rubber transferase to effectively compete for FPP and IPP substrates and the plant to make high molecular weight rubber even in the summer time, when other enzymes compete for both of these monomers. In contrast, neither of the two laticiferous species, H. brasiliensis or F. elastica, shows this behavior, indicating that the laticifer regulates molecular weight in these species, rather than the rubber transferase itself.
Figure 6. Hill plot of IPP (v) kinetics plotted against log [FPP]. The linear dashed black line indicates Michaelis-Menten kinetics.
Similar to the control exerted by FPP binding (negative cooperativity), the initiation of rubber synthesis catalyzed by the rubber transferase complex also is regulated by the divalent cation magnesium. The differences in [A]maxMg2+, defined as the concentration of activator required for maximum velocity, observed in rubber transferase complexes correlate well with the actual endogenous Mg2+ concentrations in the latex of living plants. Consistent with these data, kinetic analyses have demonstrated that FPP-Mg2+ is the active substrate for rubber molecule initiation, although free FPP and Mg2+ can interact independently at the active site.
Once rubber synthesis has been initiated, Mg2+ can still interact independently at the active site with KdIPP-Mg < KdE-Mg. Unlike FPP, however, IPP alone is not able to interact independently with rubber transferases, and IPP-Mg is the only monomeric substrate utilized in the polymerization reactions responsible for rubber chain elongation. In vitro, the concentration of Mg2+ radically affects the affinity of the H. brasiliensis rubber transferase for IPP∙Mg (Fig. 7 and Table 2) and to a lesser extent in P. argentatum, further supporting a regulatory role for Mg2+ concentration in rubber chain elongation. The metal ion cofactor concentration also affects the molecular weight of the rubber produced by all three rubber-producing species.
Figure 7. Effect of IPP.Mg concentration on the IPP incorporation rate in Hevea brasiliensis purified, enzymatically-active rubber particles.
Table 2. Variation in KmIPP.Mg in H. brasiliensis and P. argentatum with Mg2+ concentration
Hevea brasiliensis Parthenium argentatum
Mg (mM) KmIPP.Mg KmIPP.Mg
SEa SEa
μM μM
4 8000 600 1700 250
8 68 10 120 45
10 - - 140 35
30 970 70 - -
a SE = standard error
The above data indicate that endogenous Mg2+ is likely very important for latex yield and quality. Thus, internal Mg2+ levels are an attractive parameter for targeted optimisation using agronomic procedures (i.e. adding magnesium fertilizer or a chelator) to maximize plant rubber production.
Figure 8. Metabolic map of rubber synthesis in plant cells. IPP (isopentenyl pyrophosphate), the rubber chain monomer essential for chain elongation (pathway in red) is synthesized via either the mevalonic acid pathway in the cytosol or the MEP pathway in the plastid (rate-limiting metabolic intermediates are shown in purple). IPP and its stereoisomer DMAPP are combined to make several allylic pyrophosphates. GPP (C-10), FPP (C-15), and GGPP (C-30) are able to serve as rubber chain initiators (pathway in green) in various species, and are also the building blocks for several other compounds found in the resin of rubber producing cells (pathway in brown). Rubber synthesis occurs in the unilamellar rubber particle (yellow), requires a Mg2+ ion cofactor (grey), and is mediated by the rubber transferase protein(s) (orange).
Proteins Involved in Rubber Biosynthesis
While various rubber particle bound proteins have been implicated in rubber biosynthesis, the lack of solubilized activity has made conclusive identification of a distinct "rubber transferase" protein or proteins very difficult. Candidate rubber biosynthetic proteins have been identified through their association with enzymatically active rubber particles and/or through temporal or spatial gene expression profiling correlated with rubber biosynthesis in specific plant tissues and organs. These methods have proven less than satisfactory, however, and further work has discredited two of the primary proteins identified in these studies: the 14.6 kDa so-called Rubber Elongation Factor (REF), which actually appears to have a role in latex coagulation (a defense mechanism); and the farnesyl pyrophosphate synthase, which was touted as undergoing a stereochemical shift to become the cis-prenyl transferase "rubber transferase", but which undergoes no such structural change.
Despite these drawbacks, genetic profiling approaches have given some insight into the peptide components of the rubber synthesis machinery. For example, the small rubber particle protein (SRPP) does appear to play a role in molecular weight regulation and possibly also in biosynthetic rate. SRPP, a 23 kDa acidic protein (pI = 4.8), was first identified in H. brasiliensis. Homologs have since been identified in other rubber-producing species, including P. argentatum and T. kok-sahgys. Several lines of evidence support a role for SRPP in rubber biosynthesis. Interestingly, recent studies also have determined that SRPP plays a role in latex coagulation.
In addition to molecular cloning, several other methods, including photo-affinity substrate labeling, are currently being used to identify proteins involved in rubber biosynthesis, although these data are, for the most part, not yet published. Interestingly, these studies have identified several cis-prenyl transferases isolated from the latex of H. brasilinesis and T. kok-saghyz which may be associated with rubber particles, which have been claimed to be rubber particle-bound rubber transferases. Unfortunately, however, none of these proteins has been proven to make high molecular weight polyisoprene and their kinetic constants do not match those of rubber transferase, itself.
Closing Comments
In conclusion, natural rubber is a vitally important strategic material, which is synthesized in diverse plant species. While production of rubber to date has focused on the tropical para rubber tree, Hevea brasiliensis, other species including Russian dandelion (T. kok-saghyz), guayule (P. argentatum), and ficus (Ficus sp.) also produce rubber, and the former two are currently being explored as alternate sources of natural production. While these organisms each exhibit some species-specific differences in the tissue localization and regulation of rubber production, the basic mechanism of rubber production is conserved across species, with the synthesis of this polyisoprenoid polymer being localized to cytosolic, unilamellar vesicles containing the protein or proteins making up the rubber transferase. In order to maximize rubber production from alternate rubber species, an increased understanding of the development, composition, and regulation of the protein(s) making up rubber transferases is essential. While molecular screening and reverse genetic approaches have provided some progress in this direction, ongoing studies utilizing photo-affinity labeled substrates and protein interactome studies promise to yield further advances in the field and help to ensure a steady production of natural rubber for the use of the growing global consumer market.
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text:
Music and the Brain: Music and Memory
1/10/2018 By Megan Reich
The past which is not recoverable in any other way is embedded, as if in amber, in the music, and people can regain a sense of identity. . . — Oliver Sacks
In our last two posts investigating the fascinating realm of Music and the Brain, we explored what drives our musical preferences and some of the human body's physiological responses of listening to music. Today, we look into the connections between music and memory, and how music can serve as an agent of healing through helping sufferers of Alzheimer's Disease deal with memory loss.
Saving His Music
In a past Thursdays @ Three broadcast, and in various events in the Portland area, pianist Naomi has shared the music of Steve Goodwin, a pianist and composer with Alzheimer's. Through their project Saving His Music, Naomi has helped Steve write down and capture his music before it fades into the fog of his disease.
Alzheimer's is a form of dementia, a chronic disorder that causes problems with memory, thinking, and behavior. While the majority of people with Alzheimer's are 65 and older, Alzheimer's is not a normal part of aging and progressively worsens over time. Alzheimer's begins in the early stages with mild memory loss, but in the later stages of the disease, a patient will experience symptoms that interfere with daily life, including disorientation, mood and behavior changes, and difficulty speaking.
Steve's music, often inspired by nature, served as the soundtrack for his family's life and easily flowed from his hands to the piano. Much of it was never written down, and early onset Alzheimer's made it difficult for Steve to play piano. But by recalling moments from his songs, Steve has been collaborating with Naomi to fill in the gaps. His music, though he may struggle to get it out, still remains deeply instilled within him.
The connection between music and memory
Music has a profound connection to our personal memories. Listening to an old favorite song can take you back years to the moment that you first heard it. A 2009 study done by cognitive neuroscientist Petr Janata at the University of California, Davis, found a potential explanation for this link between music and memory by mapping the brain activity of a group of subjects while they listened to music.
Janata had subjects listen to excerpts of 30 different songs through headphones while recording their brain activity with functional magnetic resonance imaging, or fMRI. The songs were chosen randomly from "top 100" charts from years when each subject would have been 8 to 18 years old. After each excerpt, the subject was asked to answer questions about song, including whether the song was familiar, enjoyable, or linked to a specific autobiographical memory. Janata found that songs linked to strong emotions and memories corresponded with fMRI images that had greater activity in the upper part of the medial pre-frontal cortex, which sits right behind the forehead. This suggests that upper medial pre-frontal cortex, which is also responsible for supporting and retrieving long-term memories, acts as a "hub" that links together music, emotions, and memories.
These findings were supported by an earlier study, where Janata found that this very same region of the brain was active in tracking tonal progressions while listening to music. This music-tracking activity became even stronger when a subject was listening to a song associated with powerful autobiographical memories. In this way, Janata describes that listening to a piece of familiar music "serves as a soundtrack for a mental movie that starts playing in our head," calling back memories of a particular person or place.
Music therapy and Alzheimer's
The medial upper prefrontal cortex "hub" also happens to be one of the last areas of the brain to atrophy from Alzheimer's. This may explain why people with Alzheimer's can still recall old songs from their past, and why music can bring about strong responses from people with Alzheimer's, causing patients to brighten up and even sing along. In fact, a type of therapy called music therapy takes advantage of this very phenomenon.
Music Therapy is a type of non-verbal therapy that uses instruments and music to help people work through a range of emotional, cognitive, and social issues. Music Therapy can be a profound tool for healing through using the process of making and listening to music, providing people with a powerful channel for communication and expression.
How exactly does music therapy work? As we discussed in our previous post on physiological responses to music, music can act decrease anxiety and stress by affecting heart rate, breathing, and promoting the release of endorphins. But as we have discovered, music can also help bring back previously forgotten memories.
A recent study from Brown University School of Public Health found that the use of a music therapy program on long-stay nursing home residents with Alzheimer's was associated with reductions in anxiety medication, as well as improvements in behavioral and psychological symptoms of dementia. The music therapy program used in this study, Music and Memory, provides patients with personalized listening devices stocked with playlists of their favorite music. If you'd like to learn more about Music and Memory, the program was featured in the 2014 award-winning documentary, Alive Inside. I also recommend the author and neurologist Oliver Sacks's excellent book, Musicophilia, which explores the effect of music on the brain and the human condition through a series of portraits on people from all walks of life. Remember, wherever you are in life, music can be used as a power to heal and remember what matters to us.
"What Is Alzheimer's," Alzheimer's Association, Web. https://www.alz.org/alzheimers_disease_what_is_alzheimers.asp
Crystal, Howard. "Alzheimer's Disease," MedicineNet.com. Web. https://www.medicinenet.com/alzheimers_disease_causes_stages_and_symptoms/article.htm
"Music Therapy," University of New Hampshire, Office of Health Education and Promotion. Web. https://www.unh.edu/health/ohep/complementaryalternative-health-practices/music-therapy
Thomas, KS et al. "Individualized Music Program is Associated with Improved Outcomes for U.S. Nursing Home Residents with Dementia." Am J Geriatr Psychiatry. 2017 Sep;25(9):931-938. Web. https://www.ncbi.nlm.nih.gov/pubmed/28483436
Henriques, Carolina. "Music and Memory Program Decreases Medication Use and Improves Dementia Symptoms, Study Finds." Alzheimer's News Today, Web. https://alzheimersnewstoday.com/2017/06/07/music-therapy-helped-alzheimer-symptoms/
Greensfelder, Liese. "Study Finds Brain Hub That Links Music, Memory and Emotion." UC Davis, Web. https://www.ucdavis.edu/news/study-finds-brain-hub-links-music-memory-and-emotion
"About Us." Saving His Music, Web. https://www.savinghismusic.com/
Read other posts by Megan Reich
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text:
Q: bpf how to inspect syscall arguments trace_output_kern.c traces sys_write syscall and prints the pid in userland:
#include <linux/ptrace.h>
#include <linux/version.h>
#include <uapi/linux/bpf.h>
#include "bpf_helpers.h"

struct bpf_map_def SEC("maps") my_map = {
    .type = BPF_MAP_TYPE_PERF_EVENT_ARRAY,
    .key_size = sizeof(int),
    .value_size = sizeof(u32),
    .max_entries = 2,
};

SEC("kprobe/sys_write")
int bpf_prog1(struct pt_regs *ctx)
{
    struct S {
        u64 pid;
        u64 cookie;
    } data;

    data.pid = bpf_get_current_pid_tgid();
    data.cookie = 0x12345678;

    bpf_perf_event_output(ctx, &my_map, 0, &data, sizeof(data));

    return 0;
}

char _license[] SEC("license") = "GPL";
u32 _version SEC("version") = LINUX_VERSION_CODE;

sys_read has a signature of sys_read(unsigned int fd, char __user *buf, size_t count);, and currently we only see the PID. The premise of tracing is that we get to intercept, and inspect the arguments. I was trying to see the arguments that gets passed on as well.
If I change that struct S to hold a char array to hold char *buf as
    struct S {
            u64 pid;
            u64 cookie;
            char bleh[128]; //<-- added this
    } data;

it is throwing a fit:
/usr/src/linux-5.4/samples/bpf# ./trace_output
bpf_load_program() err=13
0: (bf) r6 = r1
1: (85) call bpf_get_current_pid_tgid#14
2: (b7) r1 = 305419896
3: (7b) *(u64 *)(r10 -136) = r1
4: (7b) *(u64 *)(r10 -144) = r0
5: (bf) r4 = r10
6: (07) r4 += -144
7: (bf) r1 = r6
8: (18) r2 = 0xffff8975bd44aa00
10: (b7) r3 = 0
11: (b7) r5 = 144
12: (85) call bpf_perf_event_output#25
invalid indirect read from stack off -144+16 size 144
processed 12 insns (limit 1000000) max_states_per_insn 0 total_states 0 peak_states 0 mark_read 0
0: (bf) r6 = r1
1: (85) call bpf_get_current_pid_tgid#14
2: (b7) r1 = 305419896
3: (7b) *(u64 *)(r10 -136) = r1
4: (7b) *(u64 *)(r10 -144) = r0
5: (bf) r4 = r10
6: (07) r4 += -144
7: (bf) r1 = r6
8: (18) r2 = 0xffff8975bd44aa00
10: (b7) r3 = 0
11: (b7) r5 = 144
12: (85) call bpf_perf_event_output#25
invalid indirect read from stack off -144+16 size 144
processed 12 insns (limit 1000000) max_states_per_insn 0 total_states 0 peak_states 0 mark_read 0

if sys_write is a bad (question) example, I've been also trying to trace sys_execve, which has an arg list of
asmlinkage long sys_execve(const char __user *filename,
                const char __user *const __user *argv,
                const char __user *const __user *envp);

Please point me the correct direction, thanks!
Edit 1
How do I intercept the arguments that was used for __x64_sys_execve?
When I try this below,
#include <linux/ptrace.h>
#include <linux/version.h>
#include <uapi/linux/bpf.h>
#include "bpf_helpers.h"

struct bpf_map_def SEC("maps") my_map = {
        .type = BPF_MAP_TYPE_PERF_EVENT_ARRAY,
        .key_size = sizeof(int),
        .value_size = sizeof(u32),
        .max_entries = 2,
};

//SEC("kprobe/sys_write")
SEC("kprobe/__x64_sys_execve")

/* Signature of sys_execve:
asmlinkage long sys_execve(const char __user *filename,
                const char __user *const __user *argv,
                const char __user *const __user *envp);
*/

int bpf_prog1(struct pt_regs *ctx, const char *filename)
{
        struct S {
                u64 pid;
                u64 cookie;
                char bleh[128];
        } data;

        data.pid = bpf_get_current_pid_tgid();
        data.cookie = 0x12345678;
        //bpf_get_current_comm(&data.bleh, 128);
        bpf_probe_read(&data.bleh, 128, (void *)filename);

        bpf_perf_event_output(ctx, &my_map, 0, &data, sizeof(data));

        return 0;
}

char _license[] SEC("license") = "GPL";
u32 _version SEC("version") = LINUX_VERSION_CODE;

It blows up thusly:
/usr/src/linux-5.4/samples/bpf# ./borky
bpf_load_program() err=13
0: (bf) r6 = r2
R2 !read_ok
processed 1 insns (limit 1000000) max_states_per_insn 0 total_states 0 peak_states 0 mark_read 0
0: (bf) r6 = r2
R2 !read_ok
processed 1 insns (limit 1000000) max_states_per_insn 0 total_states 0 peak_states 0 mark_read 0

A: The first part of your question was answered by pchaigno: if you extend your struct S and try to read it (bpf_perf_event_output(ctx, &my_map, 0, &data, sizeof(data));) without having initialised it, the verifier complains, because reading uninitialised memory from the kernel introduces a security risk. What you could do is, for example, zero the whole struct when declaring it:
        struct S {
                u64 pid;
                u64 cookie;
                char bleh[128];
        } data = {0};

Regarding the second part of your question with sys_execve, it turns out you cannot pass the syscall arguments to your function bpf_prog1() as you try to do. Your function should only take the struct pt_regs *ctx.
The confusion likely comes from the syntax used in bcc, where arguments are passed this way, but it is important to understand that bcc rewrites some parts under the hood, in particular this thing about accessing the arguments.
What you could use instead is the set of PT_REGS_PARM*(ctx) macros that are specifically defined to access the arguments of the probed function, from the relevant computer registers (example, definition). I think bcc also uses them when doing its rewriting job, but you wouldn't see it.

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