Infections of the brain and meninges


infectionsIntracranial infections represent serious brain diseases that occur in various forms and often may be hard to recognize in their earlier stages. A fast diagnosis is crucial for an effective treatment. Various technique of CT and MRI imaging have been developed to distinguish the symptoms in the brain and its associated tissues (see for example Hsu 2010). Radiologists recognize several categories of infections according to the origin (e.g. congenital and neonatal), location (intra-axial, extra-axial), or characters. In general, infections of the brain parenchyma, meninges and ventricles can have bacterial, viral, fungal, or parasitic origins. Bacterial infections usually develop from early cerebritis (inflammation of the cerebrum) to formation of abscesses (accumulation of infectious material and microorganisms) within the cranium. Some bacteria have more specific effects. Streptococcus pneumonia and Neisseria meningitides are common cause of bacterial meningitis (inflammation of the meninges and the cerebrospinal fluid). Tuberculomas, abscesses and tuberculous meningitis indicate presence of Mycobacterium tuberculosis (TB). Frequent viral infections are Herpes Simplex Encephalopathy involving Herpes simplex virus 1 (HSV-1), or infections induced by Human Immunodeficiency Virus (HIV) leading to cerebral atrophy and white matter disease. Fungal infections usually generate abscesses filled with fungi. Cryptococcosis and fungal meningitis are frequent fungal infections in some specific geographical regions. Examples of parasites causing intracranial infections are Toxoplasma gondii, or Taenia solium causing cysticercosis, which also leads to acquired epilepsy (see Vaccha et al. 2016). Consequences of intracranial infections could be in some cases lethal, in other cases they can cause a severe damage. For instance, infections of meninges and cerebrospinal fluid leading to meningitis can further evolve into subdural (between the dura mater and the underlying arachnoid layers) and epidural (between the meninges and the bone) abscesses, hydrocephalus (excessive accumulation of fluid in the brain), ventriculitis (inflammation of the ventricles containing and circulating cerebrospinal fluid throughout the brain), and venous thrombosis. Brain infection can be extended into the bone tissue and cause cranial pathologies like osteomyelitis or mastoiditis. Sometimes the infections can even lead to bone fractures. The origin of brain infection is often associated with traumas, when the microorganism spread from the wound into the soft tissues of the endocranium.

Stáňa Eisová


Digital Endocasts

[Book]   [Post]

Parietal lobes and tool use

The parietal lobe has a unique central location in the brain, and it is involved in higher cognitive functions. Investigating its functions and connectivity is essential to understand its role in uniquely human abilities. Two recent works have put emphasis on the importance of the parietal lobe for tool use.

Catani and colleagues investigated the intralobar parietal connectivity in human and monkey brains, using diffusion imaging tractography. In general, the patterns of white matter connectivity are similar in both species, although with some differences for areas that are distinct in humans. The larger tract connects the superior parietal lobule (SPL) to the angular and supramarginal gyri of the inferior parietal lobule, within the IPS. The authors suggest it might act to mediate the interaction between the two lobules during object manipulation, and to coordinate both dorsal and ventral visuospatial networks. The second and third larger tracts link the postcentral gyrus to the inferior parietal lobule and to the SPL, respectively. These might transmit tactile and proprioceptive information on the body orientation relatively to an object for guiding motor actions and grasp. The connection between the postcentral and the angular gyri was only observed in humans, leading the authors to highlight its role in specific cognitive functions. Particularly, its connections to SPL are key for tool use, mathematical thinking, and language and communication.

Kastner and coworkers reviewed the organization and function of the dorsal pathway of the visual system of monkey and human brains, focusing on the areas of the posterior parietal cortex within and adjacent to the intraparietal sulcus (IPS). Monkeys and humans have diverged in the functional contributions of the IPS since their last common ancestor, as some functionally-defined areas that are located within the IPS in monkeys have been partially relocated outside this sulcus in humans. The authors suggest this relocation might be due to expansion for accommodation of human-specific abilities, such as tool use. They hypothesize that humans might have developed a derived and advanced tool network from the modification of the macaque circuit for object manipulation. First, the human dorsal vision pathway must provide object shape information regardless of size and viewpoint, facilitating object recognition and mental manipulation. Second, object information is integrated with cognitive information such as working memory, allowing maintaining the information over a period of time. Finally, humans have areas that respond specifically to tool use, some of which also integrate frontal and temporal networks involved in action recognition and semantic knowledge related to tools and actions, respectively.

Both studies point at the parietal lobes and visuospatial integration as key elements for human cognitive capacity, as suggested by evidence in paleoneurology, evolutionary neuroanatomy, and cognitive archaeology.


Sofia Pedro

Sliding brains

Bruner E. & Ogihara N. 2018. Surfin’ endocasts: the good and the bad on brain form. Palaentologia Electronica 21.1.1A: 1-10.

[article]    [post]

Brian Metscher

Following bachelor’s work in applied physics at Caltech and a first career as a research engineer at NASA/JPL, Brian Metscher completed his PhD in the then-new interdiscipline of evo-devo at the University of California, Irvine. He did postdoctoral research on the development and evolution of appendages and teeth at The Natural History Museum (London) and Penn State University, and then served five years as an Assistant Professor in southern Indiana. During the summers he carried out research at Yale University and came to the University of Vienna in 2006, to set up the imaging lab in the Department of Theoretical Biology, where he is now Senior Scientist. He helped to establish X-ray microtomography as an essential method for imaging ex vivo biological samples, especially embryos and invertebrates. His lab is developing new and refined sample preparation and imaging methods, with applications including molecular imaging and imaging of specific cells types. He coordinates a MicroCT Methods Forum. Here a brief interview …

What are the basic principles of these methods mixing histology and digital anatomy?

MicroCT provides 3D images of intact samples at resolutions that overlap with what is achieved by light microscopy of sectioned material. Contrast-enhanced X-ray images give only histomorphological information, so microCT images are a powerful complement to traditional histology, which takes advantage of a vast array of stains with different tissue specificities. MicroCT gives a 3D overview and context for more detailed section-based images from histology (and also electron microscope).

So, you stain specimens before microtomographic scan … what about these staining techniques?

The familiar X-ray images of bones or teeth inside the body are possible because the dense calcium-rich materials absorb a lot more X-ray energy than the soft tissues around them – skin, muscle, and internal organs, which are made up mostly of proteins and water. To make soft tissues clearly visible in X-ray images, it helps to add a contrast agent: this can be a suspension of an iodine- or barium-containing liquid injected or swallowed, as is common in clinical radiology examinations. In the case of non-living samples (ex vivo imaging, most of what I do), the sample can be stained with a substance that actually binds to the tissues and has a higher X-ray absorption. The contrast stains used most often are inorganic iodine, phosphotungstic acid, and (less frequently) osmium tetroxide. None of these is specific to any one tissue type, but they do allow the different tissues and structures to be distinguished clearly in the X-ray images.

What kind of expertise, career, and tools are necessary to work in this field?

As with any kind of biological imaging, it is necessary to have a good understanding both of the biological systems under study and of how the imaging systems actually work. So a strong background in microscopy, histology, and image acquisition and analysis is important. And one must always complement one’s own expertise with good working collaborations with partners in other fields.

What is, at present, the most intriguing current challenge?

We would really like to make microCT imaging more tissue- and molecule-specific. Thus I have collaborative projects to test new staining methods and calibrate their functions in microCT images with histological baselines. And my lab is working on refining the antibody imaging method we published a few years ago to make this a more robust and routine method for 3D imaging of gene expression and other molecular patterns in developmental, comparative, and medical-related research.

Neuroanatomy and Tractography

NATBRAINLAB –  Homepage, Maps, and Blog

Primate Cranial Complexes

The primate skull is comprised of complexes including the cranial base, vault and facial region. How these complexes respond to different developmental and growth processes as well as varied selective pressures like diet, locomotion and sexual selection have been investigated in terms of modularity and integration. The concepts of modularity and integration concern the co-variance or independence of these complexes.

Profico et al. used several recent statistical methods to test previous research conclusions suggesting the primate cranial base and facial complex are strongly integrated. The cranium from 11 extant species of the Cercopithecoidea and Hominoidea were studied utilizing geometric morphometrics to investigate shape variation, the presence of evolutionary allometry and modularity or integration.

Shape variation of the primate cranial base and facial complex was assessed by Principal Component Analysis. Among taxa, shape variation of the cranial base reflected patterns in locomotion, cranial base flexion and the size of the foramen magnum. The shape variation of the facial complex reflected size-related and sex-linked morphology, the degree of lower and mid-facial prognathism and associated changes to narrowing of the nasal-orbital regions. Evolutionary allometry was tested by multivariate regression of size on shape and indicated the facial complex but not the cranial base was influenced by evolutionary allometry. Modularity and integration was analyzed using Partial Least Squares to test the degree of co-variation between the facial complex and cranial base which proved to be low. These combined results suggested the cranial base and facial complex complied with the concept of modularity rather than integration contrasting with previous studies.

An important reminder that although a pattern of similarity was found between Pongo pygmaeus and Hylobates lar this does not imply a close biological relationship, rather these taxa share similar cranial base and facial block morphology, potentially as a by-product of orthograde posture and the absence of quadrupedalism found in the other primate taxa with the exception of modern humans which are obligate bipeds. In light of the current findings, a more comprehensive reconsideration may be necessary of the effects from variation in the facial complex and cranial base morphology throughout primate evolution.

Alannah Pearson


Fiorenza L., Bruner E. 2017. Cranial shape variation in adult howler monkeys (Alouatta seniculus). Am. J. Primatol. [link]

Close-range Photogrammetry or Surface Scanner?

postRecently, Evin et al. 2016 have published a study comparing the accuracy of the three-dimensional reconstruction of five wolf crania using both photogrammetry and high-resolution surface scanner. For the photogrammetric images acquisition, they used an 8-megapixel (DSLR) Canon EOS 30D camera, mounted with a Canon EF 24–105mmf/4 L IS USMlens. The scanner-based 3D models were created using a Breuckmann StereoScan structured light scanner ( The resulting 3D models were compared first through visual observation, and second with the computation of a mesh-to-mesh deviation map. The pairs of models were spatially aligned (using a least-square optimisation best-fit criterion), followed by a 3D landmark-based geometric morphometric approach using corresponding analyses. The results show that photogrammetric 3D models are as accurate in terms of coloration, texture, and geometry, as the highest-end surface scanners. Minimal differences between photogrammetric 3D models and surface scanner-based models have been only identified on intricate topological regions, such the tooth row. Photogrammetry is becoming a common tool in archaeological and anthropological research. The major advantage of this technique is the speed and ease of image acquisition and reconstruction. Photogrammetry is an equally good alternative and less expensive than other more common techniques, such as structured light or surface scanners. In terms of archaeological samples conservation, photogrammetry could be in the future an excellent alternative to provide accurate replica models that can be widely accessible for research, without affecting the original collections.

Gizéh Rangel de Lázaro

Colin Groves (1942-2017)

Colin Groves (2017)

Emeritus Professor Colin Groves was an internationally-recognized and respected taxonomist in Mammalogy and Primatology. After completing his PhD dissertation at University College London in 1966 on Gorilla skull variation and taxonomy, Colin was appointed as lecturer at the Australian National University (ANU). Colin was an integral part of the ANU Biological Anthropology Department, welcoming discussions with internationally recognized researchers and undergraduate students alike, always made himself available and believed in an “open-door” policy for teaching. For me, he was an inspirational and influential mentor, teacher, colleague and friend who was an irreplaceable part of the Australian and International Primatology and Anthropology community. An online condolence book has been organised for those wishing to pay their respects.

Alannah Pearson