Motor neurons (MNs) are neuronal cells located in the central nervous system (CNS) controlling a variety of downstream targets. This function infers the existence of MN subtypes matching the identity of the targets they innervate. To illustrate the mechanism involved in the generation of cellular diversity and the acquisition of specific identity, this review will focus on spinal MNs (SpMNs) that have been the core of significant work and discoveries during the last decades. SpMNs are responsible for the contraction of effector muscles in the periphery. Humans possess more than 500 different skeletal muscles capable to work in a precise time and space coordination to generate complex movements such as walking or grasping. To ensure such refined coordination, SpMNs must retain the identity of the muscle they innervate. Within the last two decades, scientists around the world have produced considerable efforts to elucidate several critical steps of SpMNs differentiation. During development, SpMNs emerge from dividing progenitor cells located in the medial portion of the ventral neural tube. MN identities are established by patterning cues working in cooperation with intrinsic sets of transcription factors. As the embryo develop, MNs further differentiate in a stepwise manner to form compact anatomical groups termed pools connecting to a unique muscle target. MN pools are not homogeneous and comprise subtypes according to the muscle fibers they innervate. This article aims to provide a global view of MN classification as well as an up-to-date review of the molecular mechanisms involved in the generation of SpMN diversity. Remaining conundrums will be discussed since a complete understanding of those mechanisms constitutes the foundation required for the elaboration of prospective MN regeneration therapies. Motor neurons (MNs) are neuronal cells located in the central nervous system (CNS) controlling a variety of downstream targets. There are two main types of MNs, (i) upper MNs that originate from the cerebral cortex and (ii) lower MNs that are located in the brainstem and spinal cord. Among the latest, spinal MNs (SpMNs) have been intensively studied during the last decades and therefore provide an interesting framework for further molecular characterization. SpMNs are located in the ventral horn of the spinal cord and control effector muscles in the periphery. They form the ultimate and irreplaceable component of the neuronal circuitry since there is no alternative route to convey the commands from the processing centers located in the CNS to the effector muscles in the periphery. Their axon extending through several meters in mammals constitute an exceptional and unique anatomical feature. SpMNs are therefore the longest known cell type.Complex movements such as walking or grasping require the cooperation of several dozens of muscles. Additionally, sensory-motor feedback loops are essential for the real-time tuning of gestures. To ensure such refined coordination, SpMNs must acquire and retain the identity of muscles they innervate as well as be integrated in a coherent and functional neuronal circuitry. Hollyday et al.  and LandMNs are exceptional cell types that can be divided into two main categories according to the location of their cell body: (i) upper and (ii) lower MNs. Upper and lower MNs must be considered as distinct entities despite of their shared nomenclature. Table Upper MN cell bodies are located in the pre-motor and primary motor region of the cerebral cortex also known as the “motor strip.” Since upper MNs make glutamatergic connections with lower MNs located in the CNS, they are exclusively confined to the latter. Typical clinical symptoms of upper MN lesion include uncontrolled movement, decreased sensitivity to superficial reflex stimulation and spasticity  as well as from interneurons (INs). Paralysis is a typical clinical symptom of lower MN lesions since once damaged there is no alternative route to convey the information to the muscle targets in the periphery. Lower MNs are classified into three groups according to the type of target they innervate: (i) branchial, (ii) visceral, and (iii) somatic MNs.Branchial MNs are located in the brainstem and form, together with SNs, the cranial nuclei. They innervate branchial arch derived muscles of the face and neck through 5 cranial nuclei: the trigeminal (V), facial (VII), glossopharyngeal (IX), vagus (X) and accessory (XI) nerves. Despite their similar function, muscles of the neck and the face differ from other skeletal muscles in their embryological origin since they do not derive from the somites, but instead from the branchial arches. Such developmental difference is mirrored by specific characteristics reviewed in depth by Chandrasekhar .Visceral MNs belong to the autonomic nervous system (ANS) responsible for the control of smooth muscles  and glands. The ANS can be described as the association of two components: (i) preganglionic MNs located in the CNS connected to ganglionic neurons belonging to the peripheral nervous system (PNS). In turn, peripheral ganglionic neurons target to the final effector organ. Additionally, the ANS is anatomically and functionally divided into two structures: (i) the sympathetic system and (ii) the parasympathetic system.Motor neurons of the sympathetic system. The sympathetic nervous system is involved in the traditional “fight or flight” responses, recruiting energy storage, increasing awareness, and leading to a global activation of the body metabolism. Central MNs of the sympathetic system are located in the spinal cord from the thoracic segment 1 (T1) to the lumbar segment 2 (L2). These MNs have an intermedio-lateral position and constitute the preganglionic column (PGC) that will be described below. They connect to 3 different targets: two chains of ganglia adjacent to the spinal cord named (i) paravertebral and (ii) prevertebral as well as directly to (iii) the chromaffin cells of the adrenal medulla responsible for the release of the catecholamines  in the circulation, in response to stress stimuli. On the other hand, paravertebral and prevertebral ganglia connect to a wide variety of targets including the heart, lungs, kidneys, intestines and the colon.Motor neurons of the parasympathetic system. The parasympathetic system controls glands secretion and activates the gastrointestinal tract as well as sexual behavior, which are summarized as “rest and digest” functions. Central MNs of the parasympathetic system are located in the brainstem and contribute to the formation of the cranial nerves . Parasympathetic MNs are also found in sacral segments 2 to 4 (S2–S4) of the spinal cord. They innervate ganglia located in the proximity of the peripheral targets such as the heart, bladder, lungs, kidneys, and pancreas.In summary, visceral central MNs from the sympathetic and parasympathetic systems relay information from the CNS to ganglionic neurons of the PNS. In turn those ganglia antagonistically control a large number of various visceral targets. In contrast to branchial mentioned previously and somatic MNs described below, visceral MNs do not directly connect to the final effector. As a result, they constitute an anatomical and functional exception among lower MNs.Somatic MNs are located in the Rexed lamina IX in the brainstem and the spinal cord and innervate skeletal muscles responsible for movements Rexed, . MNs forThree classes of muscles can be anatomically and functionally distinguished: (i) cardiac muscles, (ii) smooth muscles and (iii) skeletal muscles. Cardiac muscles are responsible for the rhythmic contraction of the heart while smooth muscles control the diameter of blood vessels and the internal digestive and secretion organs. Both smooth and cardiac muscles are innervated by the ANS (described above). In contrast, somatic MNs exclusively innervate skeletal muscles that are the most abundant muscle class, with around 639 different muscles in the human body  alpha, (ii) beta and (iii) gamma that will be further described below.Alpha motor neurons. Alpha MNs exclusively innervate extrafusal muscle fibers and are the key of muscle contraction  static, innervating nuclear chain fibers and static nuclear bag fibers and (ii) dynamic, innervating the dynamic nuclear bag fibers  receive input information from the periphery and transmit it either directly to alpha MNs located in the ventral horn (monosynaptic connections) or to association neurons  that, in turn, process and convey the information toward the MNs. MNs then stimulate their respective effector that will generate the appropriate output response  the endoderm, (ii) the mesoderm, and (iii) the ectoderm. Individual layers generate progenies restricted to a limited number of distinct fates. The ectoderm undergoes a process called neurulation in which it folds inward and leads to the formation of three ectodermic masses: (i) the neural tube, (ii) the neural crest cells, and (iii) the external ectoderm. The external ectoderm generates the epidermis whereas the neural crest cells form the peripheral ganglion, the pigments of the skin as well as the dorsal root ganglia. Finally, the neural tube gives rise to the CNS, composed of the brain and the spinal cord     protein OLIG2  , the growth differentiation factor 11 (GDF11 or BMP-11), members of transforming growth factor beta (TGFB) family as well as RA    has been shown to be required for proper SAC MN generation  Figure  where thIsl1 gene to maintain its expression . However, these cells belong to the parasympathetic system (rest and digest) while thoracic PGC MNs belong to the sympathetic autonomic system (fight or flight). In addition to these functional differences, thoracic and sacral PGC MNs also differ in terms of axonal projections. While thoracic PGC MNs connect to the sympathetic chain ganglia located in the proximity of the spine, sacral PGC MNs connect to ganglia in the vicinity of the effector targets . Therefore, the molecular properties of sacral PGC MNs that remain largely unknown are presumably substantially different from thoracic PGC MNs.Initially the MMC had been separated in two divisions: (i) a medial MMC (MMCm), described above as MMC, targeting to axial musculature and present all along the rostro-caudal axis and (ii) a lateral MMC (MMCl) targeting to the body wall and present only in the thoracic segments  and Latissimus dorsi (LD) muscles and induces the expression of ETV4 in the corresponding MN pools  is secreted by both Together these results illustrate the coordination between intrinsic and extrinsically-induced cues. While the first group allows MN development independently of the environment, the second ensures the completion of essential steps. Together these mechanisms create a flexible process allowing MNs to adapt to environment variability. By definition, MN pool specification is intimately linked to axonal targeting. Intensive works have identified various molecules involves in SpMN axonal targeting. We will dedicate the next section to the review the known molecular mechanisms controlling SpMN axonal targeting.Axonal targeting is a critical process of MN development. MN axons emerge within the CNS and transit through different tissues to reach and connect to their specific muscle target in the periphery. Axonal targeting not only provides to MNs their unique anatomical characteristic and therefore their irreplaceable function but also ensures their persistence through the action of trophic signals. In order to complete such critical process, MNs combine several mechanisms in a stepwise manner Figure . SeveralThe very first choice SpMN axons make occurs within the spinal cord . MNs are intrinsically competent to recognize and connect to either fast or slow muscle fibers . Subsequently, while SpMNs strengthen their motor identity, they segregate into anatomical columns termed motor columns. Combinations of LIM homeodomain proteins provide a unique molecular profile for each motor column. In parallel, the LIM code induces the initial steps of a crucial process: MN axonal targeting. SpMN axonal targeting and further differentiation occurs in a step-wise manner. Checkpoints are established along the route to ensure the completion of critical steps. Furthermore, these checkpoints are informative and instruct developing SpMNs of the environment at the growth cone. The SpMN target can be seen as the last checkpoint of the chain. Upon reaching their final destination, SpMNs are required to complete their differentiation process and form functional connection with their target. SpMN identity echoes muscle fiber type properties. Finally, as a mechanism controlling the integrity of SpMN development, naturally programmed cell death induces the elimination of inadequate MNs and ensure the formation of a coherent circuitry.Olig2 mRNA  oriented investigation of downstream targets of known intrinsic regulators such as LIM and/or HOX proteins for example and (ii) unbiased screenings combining, viral retrograde tracing (Stepien et al., rhomboideus MN pool. These neurons constitute, in fact, the only known exception to the MN columnar organization described earlier. Although innervating an axial muscle, this MN pool is located in the lateral component of the ventral horn at caudal brachial segments; a position typical of LMC MNs (Straznicky and Tay, SpMNs are anatomically well organized. This morphological arrangement correlates with the position of their respective target in the periphery as reviewed by Kania . Thus, SFinally, this review deliberately focused on SpMN development from a motor perspective. However, SpMNs are “only” one constituent of a larger coherent circuitry. Complex movements require the control of individual muscles in a collaborating manner. This coordination relies on a highly organized circuitry between SNs, association neurons, and SpMNs as reviewed by Ladle et al. . In a peNicolas Stifani reviewed the relevant literature, wrote the manuscript and generated the figures.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Studies have shown that communication in the ICU is related to the cultural background of all involved actors. As a consequence, hospitals in multiethnic areas in western countries are currently forced to rethink their models of communication as they are increasingly transformed into spaces of cultural encounter. During this process one needs to be aware of the cultural differences in attitudes and experiences towards communication in critical medical situations. However, the growing academic interest in intercultural relations in the critical care has not yet led to the construction of cumulative knowledge. The aim of this study is to review the experiences of the involved actors, namely the care providers, the patients and their family members, with cultural diversity during the process of communication and decision-making in the ICU.A literature review was conducted. PubMed was searched. The following combinations of Mesh terms were used: [(decisionmaking) OR (communication)] AND (intensive care) OR (intensive care units)] AND [ OR  OR (migrants) OR (culture) OR (ethnicity)]. A total of 111 studies were retrieved. We excluded nonempirical studies, studies not written in English and articles published before 2003. After screening the titles and abstracts 12 articles were selected. The full text of these articles was analyzed and synthesized with a thematic-synthesis approach. During the process we performed additional searches based on the bibliographies of all the relevant articles.Culturally specific expectations about communication and decision-making, different views on gender roles, organization of the care and expression and resolving emotional and social crises may cause extra stress. The communication becomes more complex when the language of the care providers differs from the language of the patient and family. Intercultural communication can be improved by specific actions such as ethnic matching, using an interpreter and the formation of cultural-competent healthcare professionals.There is a lack of knowledge regarding the specific experiences of patients, families and care providers with communication and especially decision-making in multicultural ICUs in Western Europe.


Cherubism is a self-limiting non-neoplastic autosomal dominant fibro-osseous syndrome of the jaws. It is occasionally manifested before the age of two years. It occurs in children and more often in boys. It is characterized by notable clinical bilateral swelling of the cheeks due to a bony enlargement of the jaws that impart a characteristic ‘cherubic’ look. Regression occurs in the course of puberty leaving a few facial deformities and malocclusion. Cherubism might occur in solitary cases or in several members of the family, often in many generations. The reported case is an example of solitary sporadic occurrence within a family, which is a rarely documented condition in the literature. Cherubism is a rare, inherited disease of children which is characterized by bilateral painless mandibular and often maxillary swelling that results in a fullness of cheeks, firm protuberant intraoral alveolar mass, and displaced or missing teeth. Cherubism is inherited with a penetrance of almost 100% in males and nearly 50-75% in females . It is aA 15-year-old female patient reported to the Oral Medicine unit with complaint of bilateral swelling of the face for the past three years. The swelling started initially as smaller in size at nine years of age, which gradually increased in size to the present size. The patient agreed to participate and was explained the nature and objectives of this study, and informed consent was formally obtained. No reference to the patient's identity was made at any stage during data analysis or in the report. Family history did not reveal any previous records regarding cherubism in the other members of the family. On extra-oral examination, facial asymmetry was identified Figure . DiffuseThe teeth present were displaced from their normal position, with multiple missing teeth in mandible and maxilla. Expansion of the buccal and lingual cortical plate was noticed, and the overlying mucosa was normal. Laboratory investigations showed an elevated serum alkaline phosphatase value of 188 IU/L . Serum calcium and phosphorus levels and other investigations were within normal limits. Panoramic radiograph revealed multiple radiolucencies involving the bilateral maxilla and mandible along with the coronoid process and unerupted and displaced permanent teeth Figure .Computed tomography showed a well-defined multilocular radiolucent lesion resulting in the thinning and expansion of the buccal and lingual cortical plates, involving the entire mandible, maxilla, and lifting of the floor of the orbit Figure .A three-phase bone scan was done with 10 mCi of 99MTc-MDP injected IV and blood-pool images were taken immediately. Static images were taken three hours later. Blood-pool images revealed increased vascularity in the region of the mandible and maxilla, suggestive of an infective or inflammatory pathology. A static whole body bone scan showed increased radiotracer uptake in the maxilla and mandible Figure . PhysiolClinical or radiographic features of cherubism are not noticeable prior to fourteen months to three years of age. Characteristically, the earlier the lesion appears, the more abruptly it progresses. This patient first reported clinical swelling at the age of nine years. The progressive swelling of the face with marked increase in fullness of the cheeks is due to expansion of underlying bony structures. The bilateral enlargement of the maxilla contributes to cherubic analogy by exposing sclera causing ‘eyes raised to heaven’ look. In the present case, sclera was not prominently exposed, and hence, the ‘eyes raised to heaven’ feature was not noticeable. Radiologically it shows peculiar bilateral multilocular cystic expansion of the jaws. The presence of unerupted teeth and the destruction of the alveolar bone may cause displacement of teeth, resulting in a ‘floating tooth syndrome’ appearance . In our This patient was classified as Grade III subtype of cherubism with involvement of the coronoid process. Multiplane and three-dimensional CT imaging elucidate the accurate extent of the disease. Magnetic resonance imaging (MRI) features of cherubism described in the literature are nonspecific, but it is useful in clarifying the extent, particularly proximity of the cherubic lesions to the orbits and the optic nerves -6. In ouCherubism is usually a self-limiting condition and regresses with age. Treatment depends on the clinical course of the disease and is suggested only in the cases of esthetic or functional needs. Most investigators preferably rely on waiting until the end of puberty before planning for any surgical intervention. Surgery is indicated only in aggressive cases with functional impairments like speech, chewing or swallowing, ocular disturbances, or with the presence of significant facial deformities that may affect the patient’s psychological state. Meticulous extraoral and intraoral examinations along with radiographs help in confirming the diagnosis of cherubism, prompting an early diagnosis and management of the disease.


Certain nasal neoplasms, such as ectopic menigioma, present as nasal polyps, together with similar symptoms. The present study reports the diagnosis and treatment of ectopic meningioma in the bilateral nasal olfactory cleft in order to improve the diagnosis and treatment of ectopic meningioma in the nasal cavity. By retrospectively analyzing the clinical data and reviewing the associated literature, a detailed introduction to the clinical manifestation, diagnosis and treatment of ectopic meningioma of the nasal cavity was ascertained. The tumor was removed from the sinus by functional endoscopy surgery. Regular follow-up appointments were scheduled every three months, with no evidence of recurrence to date. The olfactory recovery and nasal ventilation were normal subsequent to surgery. Meningiomas are infrequently occurring tumors with unpredictable clinical behavior. A clear understanding of the etiology and appropriate diagnostic and management principles may aid in overcoming the challenges of treating primary extracranial meningiomas. Primary and secondary ectopic meningiomas are rare lesions . In addiMeningiomas account for 10–15% of all intracranial tumors , but priExtracranial meningiomas of the sinonasal tract are rare tumors that are frequently misdiagnosed, resulting in inappropriate clinical management. Primary extracranial meningiomas are likely to arise from the transformation of embryonic arachnoid cell remnants of ectopic meningocytes, which are derived from pluripotent mesenchymal cells. The diagnosis of extracranial primary meningiomas requires confirmation by computed tomography (CT) to exclude the presence of an intracranial mass or any underlying bony erosion of the skull base . TreatmeA 60-year-old female presented to the Otolaryngology Department of the Shanghai Pudong New Area Gongli Hospital  with hyposmia that had been present for a six-month period, without rhinorrhea or epistaxis. Clinical examination did not identify a nasal obstruction, and the patient did not possess a history of headaches or visual problems. Endoscopy identified the presence of a neoplasm in the bilateral olfactory cleft, with the nasal polyp morphology necessitating a radiological examination.A magnetic resonance imaging (MRI) examination in the Radiology Department of Shanghai Pudong New Area Gongli Hospital revealed sphenoid sinusitis on the left side of the olfactory cleft and a high-density shadow in the bilateral olfactory cleft five months prior to presenting at the Otolaryngology Department, where a CT scan of the paranasal sinus was conducted. Radiological examination of the nasal cavity prior to surgery identified the presence of soft tissue shadows in the bilateral olfactory cleft area and sinusitis in the left side of the sphenoid. MRI and CT scans of the orbit and nasal cavity revealed that the soft tissue mass was situated exclusively in the bilateral olfactory cleft region and did not invade other sinuses or the orbit .The histopathological appearance of the lesion was meningothelial, a common tumor type in which the cells present in a lobulated arrangement and are spaced along collagen fibers. The tumor cells also varied in size. They demonstrated a high nucleocytoplasmic ratio and a marginal oval nucleus, with nucleoli discernable in each cell. Fibroblasts were arranged in a matrix rich in collagen and crosslinking reticular fibers. Spiral structures were visible and did not contain psammoma bodies. Mitosis was inconspicuous, and no necrosis was observed  and 3.Immunohistochemical examination identified the presence of the epithelial membrane antigen expression. However, the immunoreactivity was focal and generally weak, identifying only a small number of positive cells in the sample examined. Other epithelial markers were also identified, including the S-100 protein in the nucleus and the cytoplasm. Isolated tumor cells were stained for the expression of Ki-67 in the nucleus.The tumor was excised from the sinus by functional endoscopy surgery. The patient continues to experience disease-free survival seven months subsequent to surgery. Post-operative nasal endoscopic examination revealed no residual mass. Follow-up visits were scheduled every three months, with no evidence of recurrence to date. The patient’s olfactory recovery and nasal ventilation were normal subsequent to surgery.The present patient presented with a benign primary ectopic meningioma. Meningiomas of the nasal cavity, particularly in the olfactory cleft, are rare. Primary ectopic meningiomas are challenging to diagnose, partly due to the infrequency of their presentation and often being confused with nasal polyps. However, primary ectopic meningiomas tend to be aggressive. Definitive diagnosis requires histological examination. Anosmia is among the first symptoms associated with ectopic meningioma, although patients also present with headaches or visual problems . EndoscoPrimary extracranial meningiomas of the head and neck are rare, with the majority presenting at secondary locations relative to the primary intracranial tumor. Primary extracranial meningiomas account for 1–2% of all meningiomas and are generally associated with a favorable prognosis. Subsequent to the diagnosis of a meningioma, it is necessary to exclude meningioma of the neuraxis or a primary central meningioma .The most frequent extracranial sites reported for primary meningioma are the nasal cavity, paranasal sinuses, cranial bones, middle ear, scalp and soft tissues of the face and neck, and the parotid gland . The larThe etiopathogenesis of extracranial meningiomas involves the migration of arachnoid cells derived from the neural crest. However, additional mechanisms have been proposed. For example, extracranial meningiomas may potentially originate from: i) Arachnoid cells of nerve sheaths emerging from the skull foramina; ii) pacchionian bodies that have been displaced or entrapped in an extracranial location during embryological development; iii) arachnoid islets that have been displaced due to trauma or cerebral hypertension; and iv) undifferentiated mesenchymal cells .et al ; atypical with frequent mitosis (Grade II); and anaplastic with invasion (Grade III). However, Zulch  suggesteet al . Acc. Accet aet al .Radical surgical resection has been associated with a good prognosis in patients with meningioma, but the benefit of adjunctive post-operative radiotherapy has not yet been established . RadiothNovel techniques available for meningioma management include proton irradiation and stereotactic radiosurgery using a gamma knife. Incomplete tumor removal, atypical or malignant tumors, nucleolar prominence, more than two visible mitotic events per 10 high-power fields and a heterogeneous contrast enhancement on CT are associated with increased rates of recurrence .Meningiomas are infrequently occurring tumors with unpredictable clinical behavior. A clear understanding of the etiology and the appropriate principles for the diagnosis and management of these lesions may aid in overcoming the difficulty of treating primary extracranial meningiomas. The present case revealed that CT and immunohistochemical examination are important for the diagnosis of ectopic meningioma of the nasal cavity and that tumor resection presents the optimum treatment for meningiomas.


A 23-year-old man presented to the emergency department following a witnessed assault. On presentation, he complained of lower facial pain, malocclusion, and numbness of the lower lip.What are the clinical signs and symptoms of mandibular fractures?What are the general principles for operative management of mandibular fractures?How should teeth in the line of mandibular angle fractures be managed?How should combined fractures of the mandibular angle and parasymphysis be managed?-The most common symptoms of a mandible fracture are pain at the fracture site and subjective malocclusion.1The goals of treatment of mandibular fractures are trifold: restoration of premorbid occlusion, early return of function, and acceptable cosmesis. The basic sequence of management via open reduction requires 4 steps: restoration of premorbid occlusion, exposure of the fracture site(s), reduction of the fracture(s), and application of fixation. Restoration of the premorbid occlusion is typically done with application of intermaxillary fixation using Erich arch bars or intermaxillary fixation screws. Exposure can be done intraorally  or extraorally (complex fractures or subcondylar injuries). Once the fractures are exposed and reduced, fixation is applied.-Management of teeth in the line of fractures remains a controversial subject. Generally, teeth in the line of fractures should be removed if they are fractured, obviously infected, or interfere with reduction of the fracture.1-More than 50% of mandibular fractures are bilateral. Combined mandibular angle and body/parasymphysis fractures should be managed with rigid fixation at the body fracture with nonrigid fixation (Champy technique) of the angle fracture.3This patient was managed with open reduction and internal fixation at both sites. He was placed into intermaxillary fixation using Erich arch bars, and both fracture sites were exposed via intraoral vestibular approaches . The lef


They act within complex topographical relationships between the sites of Ca2+ influx and those sites where the Ca2+ controlled effector proteins are located. These topographies are dynamically shaped by protein-complexes and the spatio-temporal extent of Ca2+ elevations within these topographies is controlled by Ca2+ buffers. Ultimately, these spatio-temporal relationships determine the details of Ca2+ induced effects. This e-book deals with the significance of localized synaptic calcium signaling.CaWang and Augustine review the concept of local presynaptic Ca2+ signaling domains and their functional importance for release, focusing on two giant presynaptic terminals, the squid giant synapse and the calyx of Held. Central concepts that still dominate our view about the significance of presynaptic Ca2+ domains were originally developed using these two synapses. The authors describe the distinction between nano- and micro-domain topographies and the evidence for a developmental regulation of Ca2+ domains at several synapses.Synaptic information transfer begins with presynaptic transmitter release. Brachtendorf et al. analyzed mechanisms of facilitation at individual PF-PC synapses of calretinin mutant mice using paired patch-clamp recordings. They suggest that a Ca2+-driven process that rapidly replenishes releasable vesicles operates more effectively in the absence of calretinin, thereby explaining the persistence of facilitation.A synapse that operates with nano-domain influx-release coupling is the parallel-fiber (PF) to Purkinje cell (PC) synapse. These synapses show use-dependent facilitation that surprisingly persists in mutant mice lacking calretinin—the major buffer of PF terminals—which leads to increased release probability. Orduz et al. In their study, knocking out calbindin, a calcium binding protein (CaBP) related to calretinin, had surprisingly little effect on the amplitude of postysynaptic potentials (PSPs) at PC-to-PC synapses. Their detailed study of presynaptic morphology revealed larger boutons and AZs and a higher number of docked vesicles in the mutants. The authors view these changes as a compensatory mechanism to maintain central characteristics of release in the face of a major perturbation.How critical the maintenance of calcium homeostasis on synaptic function can be is demonstrated by Timofeeva and Volynski shed light onto an often-overlooked candidate for the control of neurotransmitter release, Calmodulin (CaM). Acting as a buffer, CaM can influence calcium concentration near the AZ. The authors demonstrate that the fast calcium binding properties of CaM combined with its mobility inhibit vesicular release and favor short term facilitation during repeated action potential (AP) firing.For a given topology, CaBPs are key controllers of synaptic efficacy. Whether they simply act as buffers or have an additional sensor function is a critical question. Using constrained modeling, Matthews and Dietrich review and discuss the role and the properties of immobile or poorly mobile buffers, demonstrating that they also participate in the control of the apparent diffusion of free calcium and its decay time constant.Many studies have established how CaBPs shape the calcium wave in the presynaptic bouton or the dendritic spines. Indeed, the mobility of CaBPs will determine how they influence calcium dynamics. De Jong and Fioravante review how this wave is translated into actual vesicular release. They described the mechanisms by which the calcium sensors expressed in the presynaptic compartment undergo conformational changes when calcium binds to specific domains and the role of specific candidates in the control of vesicular release.The combination of calcium influx, extrusion, and buffering result in the calcium wave that triggers release Paul et al. reveal an unexpected interaction between the AZ protein Bruchpilot and synaptotagmin. They find that in Drosophila differentiation of neuromuscular junctions require concerted action of both Bruchpilot and synaptotagmin to result in structurally and functionally normal synapses. This study exemplifies how the combination of physiology and high-resolution microscopy can be harnessed to elucidate synaptic function at the nanometer scale.A calcium sensor central to synaptic release is synaptotagmin. Using a combination of electro-physiological recordings and super-resolution microscopy, Ehmann et al. point out in their Perspective, without direct microscopic access to the synaptic fine structure, our picture of the function of the surrounding protein networks will remain incomplete. Due to the diffraction-limit for light investigations of the AZ ultrastructure have been restricted to EM, which however provides only a static snap-shot. The authors explore, how recent advances in super resolution light microscopy like STED and STORM bridge the gap between EM and conventional light microscopy.Estimates of nano-scale topographical relationships at AZs are often derived by combining quantitative physiological techniques with modeling approaches. However, as Truckenbrodt and Rizzoli review the controversy about the mechanism of spontaneous exocytosis. It is thought that either spontaneous fluctuations in local calcium trigger fusion of vesicles residing in the same vesicle pool that normally fuses during an AP albeit via a different release sensor, or else that release is driven from a separate pool of synaptic vesicles probably independent of Ca2+. The authors speculate on the origins of this controversy and suggest that a potential solution could be related to developmental effects.Next to AP triggered release, vesicle exocytosis also occurs spontaneously at most synapses. Althof et al. demonstrated that inhibitory and excitatory synapses in the CA1 area of the hippocampus share a common spatial organization.Neurotransmitter release is highly influenced by the structural organization of calcium channels. Notably, the distance and the spatial organization between synaptic vesicles and calcium channels affect the probability of release. Using high-resolution freeze fracture immuno-EM and automatized reconstruction of Cav2.1 channel distribution, in the presynaptic compartment, the central role of these parameters is of course not limited to the presynapse.While the papers above focus on the role of calcium topography and dynamics Anwar et al. explore the expected variance of calcium concentrations due to differences in dendritic diameter using a modeling approach. In addition the authors demonstrate how to implement diameter-dependent effects on calcium signaling in the NEURON simulator. Armed with this knowledge researchers will be able to include such strong morphological effects in their models of dendritic function.The amplitude and time course of dendritic calcium transients are not only determined by buffering and extrusion, but also by morphology, specifically the dendritic diameter. Delvendahl et al. analyze the electrotonic compactness of these minute neurons. They find that GCs are electrotonically extremely compact, making them ideally suited for the efficient transfer of high-frequency information.To close the cycle of information flow, PSPs generated by synaptic inputs are conducted to the soma. How strongly these PSPs are filtered and attenuated is to a larger part determined by the electrotonic compactness of the dendritic branch. Using whole-cell recordings directly from the dendrites of cerebellar granule cells (GCs), 2+ functions arises from the localization of Ca2+ signals to specific sub-compartments by the joined action of topographical relationships with CaBPs and emphasize the importance of technical breakthroughs in promoting our understand compartmentalization.This research topic gives a prospect onto how the multitude of synaptic CaAll authors listed, have made substantial, direct and intellectual contribution to the work, and approved it for publication.This work was supported by an ARN grant to PI (FRM 2014 DEQ20140329514) and a DFG grant to HS (SCHM1838).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


A 34-year-old African American man presents to the emergency department after an accident with a high-speed motorcycle. The patient was reportedly wearing a helmet. He lost consciousness and complained of pain around his right eye.Identify fractures in the patient's CT scan.What signs and symptoms are important in forming an accurate diagnosis?Describe the classification system for this type of fracture.Describe how to treat the fracture pattern in this patient.The patient suffered fractures to his nasal bone, right superior and inferior orbital rims, bilateral maxillary sinuses, and lamina papyracea, consistent with a nasoorbioethmoid (NOE) fracture pattern.Panfacial fractures may result from penetrating injury  or blunt trauma (motor vehicle collision). The severity of a facial injury is determined by the mass, density, and shape of the colliding object. Once the patient was medically stabilized and cervical spinal injury was ruled out, a complete examination of the face revealed a complex laceration of the nasal complex, telecanthus, and a ruptured right globe with absent light perception on the right side. Computed tomographic (CT) scan of the head confirmed multiple facial fractures within the nasoorbitoethmoid complex (NOE).The NOE complex represents an intricate anatomical confluence of frontal, nasal, ethmoid, and orbital bones with their associated sinus tracts. Traumatic force that disrupts the primary buttresses of the NOE complex will comminute the complex and result in telecanthus, enophthalmos, diplopia, and possible cerebrospinal fistula. The NOE classification system described by Markowitz et al (1991) is based on the anatomic relation between the medial canthal tendon and the fracture. Type I fractures represent a single noncomminuted central fragment without canthal disruption, type II fractures are comminuted but the medical canthal tendon remains firmly attached to bone, and type III fractures result in severe central fragment comminution with complete disruption of medial canthal tendon insertion. The patient described earlier demonstrated complete detachment and isolation of the right medial canthus with free floating left canthus attached to bone.Once diagnosed, the goal of treatment is surgical correction for fractures that demonstrate instability on manual manipulation or by displacement on CT scan. While the surgical approach is determined by the type of NOE fracture pattern, the focus of all NOE correction is proper insertion of the medial canthal tendon onto the bony central fragment in order to maintain the normal intercanthal distance and outward appearance of the midface. In the patient, transnasal wiring was used to position comminuted bone fragments to the medial canthal tendons and the canthi were fixated posteriorly and superiorly together. The supraorbital rim was corrected with a titanium plate, and a calvarium bone graft was harvested and placed into the lower portion of the frontal bone above the nasal root. Surgery was tolerated without complications. Enucleation of the ruptured right globe was performed on a later date.NOE fractures are complex and encompass frontal, nasal, ethmoid, and orbital anatomy. Diagnosis is obtained through CT scan, and the goal of treatment is reduction of fracture segments and reinsertion of the medial canthal tendon to avoid telecanthus.


Hearing, a central ability in our lives, allows us to distinguish the sound of birds from mosquitos, remember our favorite piece of music, have a conversation with a friend, and be alerted by a honk while crossing a road with our child. In other species, such as bats, this sensory modality is key for survival. Many researchers have dedicated their efforts to understand the auditory system. This research topic on the Functional Organization of the Auditory System brings some of the best scientific efforts to understand audition from genetic studies in rodents, electrophysiological recordings in rodents, bats, and monkeys as well as fMRI and translational research in humans. The following paragraphs aim to give a glimpse of the contents in this topic.Fuentes-Santamaría et al. study experimentally induced conductive hearing loss in rodents and found changes in microglial cells, but not astrocytes, suggesting they may be the dynamic modulators of synaptic transmission in the cochlear nucleus immediately following unilateral hearing loss. Plasticity after injury of any component of the auditory system is of obvious clinical relevance. The thorough review presented by Gold and Bajo, reveals the potential of plasticity after injury, but also the sequels at different levels of the auditory hierarchy, from the brainstem to the cerebral cortex. Auditory driven alerting behavior is critical across species and has been further characterized by Gomez-Nieto et al. providing strong evidence that the cochlear root neurons-pontine reticular nucleus pathway mediates fast neurotransmission and binaural summation of the acoustic startle reflex in the rodent. Auditory hallucinations are a distinct symptom of schizophrenia. Nakao and Nakazawa, present a rodent model of this disorder and show that the “paradoxically” high spontaneous LFP activity of the primary auditory cortex in the absence of external stimuli may possibly contribute to the emergence of schizophrenia-related aberrant auditory perception. These authors suggest that NMDAR hypofunction in cortical GABAergic interneurons leads to two temporally distinct, brain state-dependent LFP deficits in the A1 cortex. Sotoca et al. present a surprising result in a transgenic P23H-1 rat model that opens up new strategies of study on deaf-blindness implicating a direct effect on rhodopsin mutation.Hearing loss among the aging or after injuries can be very debilitating. Macaca mulatta) or cynomolgus (Macaca fascicularis) monkeys have a well-defined temporal lobe with superior temporal plane, where the primary auditory cortex lies. This proximity of the monkey brain to humans offers an exceptional opportunity for better understanding the human nervous system, and the auditory, in particular, yielding some unique access to information on the evolution of audition toward speech. A research on the electrophysiological properties of neuronal responses within the primary and belt areas of the auditory cortex to simple and complex auditory stimuli  has shown that harmonic features, such as relationships between specific frequency intervals of communication calls, are processed at relatively early stages of the auditory cortical pathway, but preferentially in LB. Detailed anatomical data on the feed-forward and feed-back arrangement of circuits of primary, belt, and parabelt areas presented by Hackett et al. showed the convergence of feedforward inputs into rostral medial belt from middle lateral belt (ML) and caudal parabelt (CPB). This was surprising given that CPB is at a higher stage of the processing hierarchy, with mainly feedback projections to all other belt areas. These data have stimulated a revision of the conventional model. Joly et al. addresses methodological issues of fMRI and anatomical mapping by means of combining information from cortical folding, micro-anatomy, surface-based atlas and tonotopic mapping. The fMRI study by Ortiz-Ríos et al. identifies the network for species-specific vocalization processing in the auditory ventral pathway, and they highlight the involvement of the anterolateral belt and parabelt areas. This fits well with our own anatomical data showing that the rostral superior temporal gyrus sends convergent input to the dorsal half of the temporal pole . It is particularly in this region of the dorsal temporal pole that neurons show working memory-related responses . Furthermore, even if monkeys can hold auditory stimuli in working memory, their ability to keep them for longer delays is very limited. The anatomical work by one of the editors  aims to explain this poor auditory long-term memory ability by demonstrating that the connections from the dorsal temporal pole to medial temporal cortex bypass most of area 36 of the perirhinal cortex, to directly reach area 35, entorhinal, and posterior parahippocampal cortices. This contrasts with the highly dense projections from the visual cortex to area 36 of the perirhinal cortex, and may explain, at least in part, the poorer auditory memory in monkeys compared with vision. These anatomical data support the hypothesis that auditory stimuli can access the medial temporal cortex if intermingled with information from multimodal areas and this may guarantee the persistence of memory traces that include auditory information .Closer to humans, non-human primates like rhesus , the ILD sensitivity depends on stimulus types . They also show that ILD sensitivity was heavily dependent on binaural levels, suggesting that with the lack of binaural level invariant encoding in A1 neurons, A1 neurons seem to encode auditory space using population codes.The study by Washington and Tillinghast show the findings in bats to support that the hemispheric specialization for speech and music in humans is based on hemispheric specialization for temporal and spectral resolution.Tanji et al. demonstrates that a lesion restricted to this auditory-responsive area is enough to cause apraxia of speech. The relevance of this result roots in that this lesion is sufficient to impair the execution of fluent speech, but leaves speech perception/comprehension intact. This result has important theoretical implications for the motor Sensory vs. Motor theories of speech. This study takes parts and bets for the sensory theory of speech. Lahav and Skoe present their work in neonatal intensive care units with the aim of better understanding the impact of the noisy sound environment on the developing auditory system as an important first step in meeting the developmental demands of preterm newborns. Su et al. present a novel method to resolve spatial organizations of human auditory cortex using a combination of EEG, MEG, and fMRI data and multivariate pattern analysis.Patient studies are of critical importance when studying the function of the nervous system. The patient with a tumor resection in the ventral precentral gyrus presented by Moerel et al. by examining tonotopic maps at a single-subject level to detail the topography of primary and non-primary areas. They merge multiple maps indicative of anatomical  as well as of functional properties  to better identify auditory cortical areas in individual human brains. Individual differences add up with dynamics of auditory representations in humans in the fMRI data on attentive vs. inattentive auditory events. Amaral and Langers show the suppressive binaural interaction during a dichotic listening, which illustrates the dynamic properties of our auditory processing.The importance of individual differences in human primary auditory cortical maps is addressed by Johannesen et al. Identifying the multiple contributors to the audiometric loss of a hearing impaired listener at a particular frequency is becoming gradually more useful as new treatments are developed.Of clinical relevance is the study by This research topic reunites a wealth of studies of diverse animal species including humans and it is our hope that they contribute to better understand mechanisms underlying audition and to achieve real-life applications in clinical populations.MM was invited to prepare this RT and invited Dr. YK to be co-editor in it. We both prepared and discussed a list of guests-authors, invited them, revised their manuscripts and handled their revisions.This study was supported by NIMH/IRP grant BFI 2003-09581 and the Spanish Ministry of Science and Innovation grant BFU 2006-12964.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Preterm birth is associated with increased risks of neurological and motor impairments such as cerebral palsy. The risks are highest in those born at the lowest gestations. Early identification of those most at risk is challenging meaning that a critical window of opportunity to improve outcomes through therapy-based interventions may be missed. Clinically, the assessment of spontaneous general movements is an important tool, which can be used for the prediction of movement impairments in high risk infants. Movement recognition aims to capture and analyze relevant limb movements through computerized approaches focusing on continuous, objective, and quantitative assessment. Different methods of recording and analyzing infant movements have recently been explored in high risk infants. These range from camera-based solutions to body-worn miniaturized movement sensors used to record continuous time-series data that represent the dynamics of limb movements. Various machine learning methods have been developed and applied to the analysis of the recorded movement data. This analysis has focused on the detection and classification of atypical spontaneous general movements. This article aims to identify recent translational studies using movement recognition technology as a method of assessing movement in high risk infants. The application of this technology within pediatric practice represents a growing area of inter-disciplinary collaboration, which may lead to a greater understanding of the development of the nervous system in infants at high risk of motor impairment. Each year more than 15 million babies worldwide are born preterm  and the number of cases continues to rise . MorbidiThere are currently no standardized clinical guidelines for the prediction of motor impairment in high risk infants and the identification of those at highest risk typically involves the integration of clinical history, neuroimaging results, different clinical assessments, and experience of health care professionals. The assessment of spontaneous general movements is an important tool, which can be used for the prediction of movement impairments in high risk infants .Movement recognition aims to capture and analyze relevant limb movements through computerized approaches focusing on continuous, objective, and quantitative assessment. Different methods of recording and analyzing infant movements have recently been explored. Camera-based solutions –10 and bThe aim of this article is to briefly summarize the current most evidence based clinical approach to observational movement assessment in high risk infants  and identify the current studies, which have applied a variety of automated movement recognition technologies to assess infant movement.Infants learn how their bodies move and interact with the environment in early infancy . This isThe development of spontaneous movements in infants has been studied and described in detail by Heinze Prechtl and colleagues . PrechtlThe application of this assessment clinically involves the evaluation of the qualities of the spontaneous general movements through Gestalt perception of the observer . A videoIn typically developing infants, spontaneous movements are characterized by large variation , 19. WriAtypical motor development is characterized by limited variation and limited variability in generalized movements . In partThe challenges of applying the GM assessment in practice relate to the availability of appropriately trained and skilled clinicians. Considerable training is required for an assessor to become reliable enough to make an accurate evaluation. The assessment is susceptible to observer fatigue  and is dDespite good levels of inter-observer reliability with the GM assessment , there wThese challenges in the early detection of motor impairments in high risk infants have led to an increasing interest in the use of automated movement recognition technologies being applied in this clinical area.The use of automated movement recognition technology has been explored in many different clinical conditions such as dementia , ParkinsMovement recognition in clinical applications aims at the automated detection, classification, and assessment of the quality of limb movements focusing on indications for abnormalities. Capturing limb movements can be based on either indirect or direct sensing . IndirecThere are considerable challenges in utilizing this technology in the neonatal environment, in particular, the size, fragility, and vulnerability of infants needs to be taken into account. Furthermore, the automated movement assessment must be sensitive and reliable enough to detect subtle changes in movements, which are the basis for clinical diagnosis.Table pre-processed [see in Ref.  different types of movements. Various classification frameworks have been reported in the context of wearable/environmental sensors such as  using three dimensional (3D) motion capture systems; and (ii) using traditional color cameras. Motion capture based systems require special markers to be attached to the limbs being tracked. High-end cameras typically provide very high 3D tracking accuracy and resolution , but at a considerable price and setup effort. These systems are most commonly seen in the research setting and due to practical limitations are not easily adaptable to the clinical environment.Meinecke and colleagues applied a motion capture system to objectively measure the spontaneous movements of infants during the first months of life . Fifty-tDespite the popularity of consumer 3D cameras such as Microsoft’s Kinect , these hStandard video cameras such as regular web-cams, RGB cameras on tripods, and even video-enabled baby monitors  have alsn = 30) report promising results (sensitivity 85% and specificity 88%) with respectable follow-up data past 4 years of age  may be more difficult to achieve due to the logistics of attaching direct sensors to small infants.The main advantage of video-based movement analysis lies in the recording of spatial data in addition to temporal measurements, which gives direct access to, for example, posture-related information. In contrast, direct sensing approaches typically have a much higher temporal resolution allowing for more detailed assessments, which is beneficial for in-depth analysis of subtle changes that may precede the development of CP.Some approaches have been developed that aim at combining both sensing methods in order to benefit from both spatial and high temporal resolution – at reasonable costs and minimum setup efforts for practical applications – for high-fidelity movement analysis . Berge aPrediction of motor impairment (such as CP) in preterm infants is challenging, and ideally requires techniques that are both sensitive and specific. Due to the large number of complex factors affecting neurodevelopment, and the difficulty in assessing brain plasticity, predicting which children will develop CP on the basis of a single assessment will always be challenging . A multiAccurate, non-invasive assessments of sufficient sensitivity to identify longitudinal changes in movement patterns could hold considerable hope for the future. This mini-review has identified recent studies employing video-based assessment, assessment through direct movement sensing and hybrid systems. Specifically, the use of accelerometry and computer vision may offer clinically feasible and promising methods of objectively measuring quality and quantity of infant movement. The application of these technologies may prove to be useful not only in the prediction of infants at highest risk of motor impairment but also in the evaluation of therapies aiming to influence the developing brain.The Guest Associate Editor Gavin John Clowry declares that, despite being affiliated to the same institution as authors Claire Marcroft, Aftab Khan, Michael Trenell, and Thomas Plötz, the review process was handled objectively and no conflict of interest exists. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.http://www.frontiersin.org/Journal/10.3389/fneur.2014.00284/abstractThe Supplementary Material for this article can be found online at Click here for additional data file.


The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH) architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average) that is homologous to fold type-I pyridoxal 5′-phosphate (PLP) dependent enzymes like aspartate aminotransferase (AAT). These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. This group occurs mainly in the Actinobacteria and Gammaproteobacteria phyla. An analysis of the multiple sequence alignments of their wHTH and AAT domains suggested the presence of specificity-determining positions (SDPs). Mapping of SDPs onto a homology model of the AAT domain hinted at possible structural/functional roles in effector recognition. Likewise, SDPs in wHTH domain suggested the basis of specificity of Transcription Factor Binding Site recognition. The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.  Bacillus subtilis [The members of the GntR family of bacterial transcriptional regulators are characterized by the presence of two domains . The N-tsubtilis , 8 confi Rhodobacter capsulatus [ Bacillus subtilis GabR [γ-amino butyric acid (GABA) activates transcription of gabT and gabD encoding GABA aminotransferase and succinic semialdehyde dehydrogenase, respectively; PdxR is involved in the regulation of the PLP synthesis in several bacteria such as Corynebacterium glutamicum [ Streptococcus pneumoniae [ Listeria monocytogenes [ Streptococcus mutans [ Bacillus clausii [ Brevibacillus brevis MocR member has been demonstrated to activate the expression of the gene coding for the enzyme d-alanyl-d-alanine ligase [The MocR regulators are widespread among eubacteria , 4 and cpsulatus ; Bacillulis GabR  in the putamicum , Streptoeumoniae , Listeriytogenes , Streptos mutans , and Bac clausii . Recentle ligase .The C-terminal domain displays a highly variable sequence within the MocR subfamily  possiblyWe provide here a bioinformatics analysis of the features distinguishing a group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. An attempt to relate specifically conserved residues in the wHTH and AAT domains to function is also reported.The reference RegPrecise database version 3.3  was util de novo identification of candidate Transcription Factor Binding Sites (TFBSs) in the training set of potential upstream region, the MEME web server [ bona fide promoter elements. Candidate DNA-binding sites were submitted to the TOMTOM and FIMO tools of the MEME suite [E-value threshold < 0.01). With the aim of checking whether the TFBSs are present in single copy through the genomes, three reference genomes  were selected and FIMO was used to scan their upstream sequence elements for individual matches for each motif.For comparative analysis of genomic regions, we excluded closely related strains; that is, if more than one regulon from different strains of the same bacterium was present in regulon dataset, only one of them was selected for further analysis . Genes encoding MocR proteins were localized in their respective genomes, and the intergenic regions putatively involved in the control of selected regulons were retrieved from NCBI GenBank . For de b server  was usedb server , specifib server  and compb server  to detecME suite . TOMTOM ME suite  and RegTME suite  and disphttp://regprecise.lbl.gov/RegPrecise/index.jsp) was queried to find all the regulons predicted to be under the control of a regulator of the MocR family. The regulons are organized in the databank according to taxonomy, orthology, and similarity of the TFBSs. A subset of MocR regulons includes genes coding for hypothetical membrane proteins of unknown function denoted as YczE (Conserved Domain Database code COG2364). These membrane proteins share with the family YitT  the presence of one or two DUF161 domains. Indeed, YczE and YitT proteins are generically annotated as “membrane proteins containing the DUF161 domain.” The YczE proteins are characterized by the absence of the C-terminal domain DUF2179 (corresponding to the PDB structure 3HLU) present in the members of the YitT family. The sequences of all the MocRs predicted to regulate YczE genes, to which we will refer as YczR, were collected (The databank RegPrecise version 3.3 (ollected . Most reollected . The Mochttp://dx.doi.org/10.1155/2016/4360285). All the sequences (YczR RegPrecise and MocR/other) were retrieved from the RefSeq databank and multiply aligned with Muscle or ClustalO programs. The wHTH and AAT domains were subsequently analyzed separately. The UPGMA method in MEGA5.2 was applied to calculate a cladogram of the aligned sequences of the MocR domains ( (vide infra).To verify whether the YczR RegPrecise set represented a real distinct group within the MocR family, all the MocR regulators not involved in YczE gene-containing regulons (MocR/other) were collected from the Actinobacteria and Gammaproteobacteria sets contained in the RegPrecise databank . Indeed, presence of synteny is another strong hint of functional association between the regulator and the adjacent divergently transcribed gene [The MocRs of other species sharing YczE synteny with those retrieved from RegPrecise databank were collected from the SynTax database . Xdet program spots the SDPs by examining the correlated mutational behavior of the positions characteristic of a subfamily. Identification of SDPs however is not a trivial task and the methods available are still poorly performing . QualityApplication of S3det analysis to the wHTH domains in the alignment of the sequence set MocR_ALL filtered at 90% sequence identity was able to independently reproduce the clustering obtained by UPGMA and reported in  bona fide SDPs those positions that were predicted by Xdet and S3det in one alignment and by one of the two methods in the other. For example, if position A was predicted as SDP by Xdet and S3det in the alignment calculated by ClustalO and by S3det in the Muscle alignment, then A would be considered an authentic SDP. If position B was predicted as SDP only by S3det in the alignment calculated by ClustalO and S3det in the Muscle alignment, then B would not be considered an SDP. S3det was able to reproduce the clustering reported in  Saccharopolyspora erythraea (RefSeq code WP_009946170) was built on the template structure α-aminoadipate aminotransferase from Thermus thermophilus (PDB code 2EGY) with which it shares 33% sequence identity . For that reason, we calculated two multiple alignments of the same sequence set with the programs ClustalO and Muscle and applied a consensus criterion: we consideredConservation of the wHTH domain of the YczR population suggests the conservation of the corresponding TFBSs upstream the YczE genes . The nucA distinctive feature of the GntR family is the presence of several TF subfamilies with very different binding motifs. Indeed, the few MocR regulators analyzed so far have revealed that the sequences of TFBSs are quite dissimilar between organisms from different taxonomical divisions, even within regulons involved in the same pathway, as in the case of PdxR . For thi Sphingobium japonicum is 629 bp long, while the other two sequences are composed of 61 and 90 nucleotides: their comparison, therefore, is affected by the length difference. In particular, the alignment of Actinobacteria promoter sequences is very fragmented, due to the great variability of sequence length, thus making the identification of conserved patterns through the sequences (data not shown) quite difficult.After elimination of species redundancy, 58 YczR regulons remained in the Actinobacteria set and 15 in the Gammaproteobacteria (Supplementary Information Table S2), while the three regulons mentioned above constituted the Alphaproteobacteria set. The average length of the intergenic regions is 100 bp (ranging from 27 to 274 bp) and 86 bp (ranging from 54 to 90 bp) for Actinobacteria and Gammaproteobacteria sets, respectively. In the Alphaproteobacteria set, the sequence fromFor Actinobacteria regulons, the motif search revealed the presence of a conserved DNA motif (GGCCA) of 5 nucleotides with an inverted repeat (TGGCC) and a spacer of 12-nucleotide length . In the  Amycolatopsis mediterranei U32, Klebsiella pneumoniae subsp. pneumoniae MGH 78578, and Sphingobium chlorophenolicum L-1 from Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria, respectively. The noncoding regions of their genomes (including both forward and reverse strand) were scanned with a score matrix derived from the alignment of the sequences from all datasets. For none of the three genomes, a significant motif was detected: only the noncoding regions intervening in the predicted YczR regulons showed a significant p value (<0.05).The search of TFBSs in the databases of known DNA-binding motifs integrated in the MEME webserver (Prodoric and RegTransBase), using as a query the single repetition and a consensus sequence of the three repetitions derived from the original alignments, did not reveal any significant match with known motifs. To prove uniqueness of candidate TFBSs through the genomes, we selected three representative organisms:GntR regulators are a relatively new and still poorly characterized family of transcription factors. Among them, the MocR subfamily is particularly interesting because of its homology to fold type-I PLP dependent enzymes and its role in the expression of genes involved in several metabolisms or in membrane transport of substrates. Since the last decade, this complex subfamily has been actively investigated but it is still far from being characterized and understood. Bacillus subtilis B3 may belong to the ABC transport system within an operon involved in the biosynthesis of the antibiotic surfactin [ Bacillus amyloliquefaciens FZB42 takes part in the regulation of the biosynthesis of the iturin antibiotic bacillomycin D [In this report, we suggest that a group of MocR regulators, predicted to regulate the expression of the uncharacterized membrane proteins YczE, can be distinguished within this subfamily by the presence of characteristic SDPs. We first confirmed that the wHTH and AAT domains of the MocR regulators, predicted by the RegPrecise databank to regulate YczE genes, cluster in the same subtree of a UPGMA cladogram built upon a multiple sequence alignment containing also MocRs from Actinobacteria and Gammaproteobacteria extracted from the same databank. Syntenic genes were afterwards identified and collected from the SynTax databank. The sequences of the MocR proteins were multiply aligned along with those previously retrieved from RegPrecise databank. Once more, both domains of the syntenic MocRs clustered in the same subtree. This pattern strongly supports the notion that the MocRs possibly involved in regulation of YczE genes share structural similarities that distinguish them from the other components of the same subfamily putatively involved in the regulation of other genes, such as those responsible for PLP biosynthesis. The YczE genes associated with divergently transcribed MocRs occur mainly in Actinobacteria and in Gammaproteobacteria. Only a few instances are observed in Alphaproteobacteria. YczE genes are widespread among bacteria and only a subpopulation is divergently transcribed with respect to MocR. Very little is known about the structure and function of YczE membrane proteins. It has been hypothesized that a YczE protein fromurfactin . More reomycin D . B. clausii, the existence of two different conformations of the regulators able to selectively bind direct or inverted repeats. Noteworthily, the motifs from the three different taxonomical groups share a substantial number of conserved nucleotides. This is an exception among the MocR TFBSs investigated so far: indeed, an unequivocal and conserved TFBS motif shared by the MocR family has not been found yet [Application of protocols to detect SDPs and inspection of the logos pointed up residues potentially playing specific structural roles in YczR wHTH and AAT domains. In the wHTH domain, several residues are putatively involved in DNA interaction. In particular, Glu28 was identified as the discriminant residue of the YczR group by the JDet analysis. This residue, putatively interacting with the DNA phosphate backbone, precedes the “universally” conserved Arg29 (corresponding to FadR Arg35 responsible for interaction with G base in the DNA major groove). Other residues are potentially involved in DNA binding . The comound yet . This reThe analysis on the AAT domains of the YczR pointed several residues characteristics of this group . Particu Bacillus amyloliquefaciens FZB42 is adjacent to genes coding for components of an ABC transporter system predicted to be involved in polar amino acid translocation [ Bacillus subtilis strain B3 has been indicated as a potential ABC transporter component although it lacks the corresponding sequence signature [The information available in the RegPrecise database prompted the analysis of the structural features of a MocR subgroup predicted to regulate the expression of membrane proteins of the family YczE with unknown function. We concluded that this MocR subgroup possesses distinguishing characteristics. Indeed, the wHTH and AAT domains display distinctive conserved positions which may be related to their specific functional properties. A subset of the YczE membrane protein populations is predicted to be under the control of regulators putatively able to respond to PLP and, very likely, amino acid binding. These considerations suggest that YczE proteins may be involved in transportation (influx or efflux) of metabolites, in particular amino acids, connected to pathways in which PLP takes somehow part. Indeed, YczE gene oflocation  within tlocation . Likewisignature . All theThe Supplementary Information contains data which could not be included in the main text because of their size. In particular: Sequence alignments among YczR and non-YczR wHTH and AAT domains; the alignments contains 254 and 281 sequences with average length of 67 and 358 residues, respectively. The alignments can only be visualized on the computer screen using a PDF reader program. The figures display the conserved positions and the position characteristic of the YczR subset compared to those of the non-YczR set; A stereo picture of the AAT domain of a homology model of a YczR displaying the predicted specificity-determining positions (SDP); A table listing the non-YczR regulators taken from the RegPrecise data bank; A table listing the YczR regulators found through the SynTax analysis; A table listing the putative organisms containing the YczR regulons used to derive the DNA binding motif. More details are described in the captions to the figures included in the Supplementary Information file.


MicroRNAs (miRNAs) have been identified as one of the most important molecules that regulate gene expression in various organisms. miRNAs are short, 21–23 nucleotide-long, single stranded RNA molecules that bind to 3' untranslated regions (3' UTRs) of their target mRNAs. In general, they silence the expression of their target genes via degradation of the mRNA or by translational repression. The expression of miRNAs, on the other hand, also varies in different tissues based on their functions. It is significantly important to predict the targets of miRNAs by computational approaches to understand their effects on the regulation of gene expression. Various computational methods have been generated for miRNA target prediction but the resulting lists of candidate target genes from different algorithms often do not overlap. It is crucial to adjust the bioinformatics tools for more accurate predictions as it is equally important to validate the predicted target genes experimentally. Caenorhabditis elegans [Drosophila melanogaster miRNAs [Since the discovery of microRNAs in the early 1990s, the view of the regulation of gene expression has started to change. The first identifications of the endogenous short regulatory RNAs in r miRNAs  revealedr miRNAs ,4. The rr miRNAs  and miRNr miRNAs . Furtherr miRNAs .The main obstacle in miRNA research is to detect the specific sequences on target genes that miRNAs are fully or partially complementary  and to dMiRNAs are short single-stranded RNA molecules which are transcribed from endogenous genes by RNase polymerase II initially as long precursors (pri-miRNAs). Pri-miRNAs vary from 70 to 100 nucleotides in size and fold into a hairpin-loop structure consisting paired bases with several mismatches and bulges . Pre-miRC. elegans [The biological processes of miRNA-regulated gene expression are various including cell proliferation, cell differentiation, apoptosis, signal transduction, immune response, stress resistance, fat metabolism, insulin secretion and hematopoiesis . In 1993 elegans . The lev elegans . Accordi elegans . In plan elegans . Althoug elegans .Inside the cell there are several features that regulate the target recognition of miRNAs. The first and the most recognized feature is the sequence specificity of miRNAs to 3' UTR of mRNAs. Even though this feature is quite limited, the AU residues in target sites increase the accessibility of the miRNAs to form duplexes . The tarFrom the moment of understanding the effects of miRNA regulation of genes, studies have been focused on predicting the accurate target genes for miRNAs and considerable number of methods has been identified so far. These methods diversify from small-scale genetic methods and high-throughput biochemical processes for target sequence isolation to computational prediction methods . The mosGenetic methods use phenotypic suppression tests for identifying miRNA target sequences. Generally, an miRNA mutant type which has a loss-of-function phenotype is constructed by traditional mutagenesis or RNAi mechanism and the candidate mRNAs are screened for suppression. In the mutant strains, target genes are repeatedly upregulated. The recognized advantage of the genetic methods is the direct relation between the identified target gene and a specific physiological process in the cell which is regulated by the miRNA. However, these methods are not qualified for distinguishing indirect targets of miRNAs or determining multiple targets that cause the same phenotype .Biochemical approaches for identifying miRNA targets are more sophisticated than genetic methods and they are usually associated with bioinformatics analyses. They have augmented the sensitivity in identifying target mRNAs endogenously. First attempts were based on immunopurification of miRNA ribonucleoprotein (miRNP) complexes, isolation of related mRNAs, and microarray analysis of target transcripts subsequently ,32. ReceComputational methods have been based on algorithms that are generated by the physical properties of miRNA regulation, subsequently as perfect Watson-Crick complementarity between the first 2–7 nucleotides of miRNA and the 3' UTR of mRNAs, evolutionary conservation, and secondary structures of 3' UTRs based on AU content. These methods generate many false positive predictions and the results need to be experimentally validated. In order to test computational predictions for functional regulation, heterologous reporter genes are fused to target 3' UTRs; however, the function of predicted sites can still remain questionably ambiguous .Using bioinformatics tools for predicting target genes is relatively a new approach regarding the challenging prediction algorithms and complexity of miRNA-target interactions. Prior to performing high-throughput experiments it is critically important to determine miRNA targets by computational methods and the complementarity between miRNA and target mRNA has been the fundamental advantage for computational analysis . In ordeComputational methods for miRNA target prediction usually start with simple algorithms that depend on Watson-Crick base pairing between the seed region of the miRNA and the 3' UTR regions of mRNA. The Ensembl database comprises 3' UTR regions for human, mouse, and zebrafish genomes that are extracted from alignments of cDNAs and expressed sequence tags . HoweverDrosophila melanogaster [Drosophila pseudoobscura and Anopheles gambiae. Subsequently, the target sites were scored and used as an input for the algorithm [The Stark method which Stark and his colleagues generated was the first miRNA target prediction tool for nogaster . The sealgorithm .The miRanda algorithm was generated after the Stark method and it hunts highly overlapped base pairing in the 3' UTRs for identifying potential binding sites . The algThe TargetScan algorithm, on the other hand, uses a different approach from the other two methods. It searches for perfect complementarity in the seed region and beyond . ComplemThe PicTar algorithm firstly uses conservation data from 3' UTRs of multiple species as input data and looks for the alignment of complementary seed regions. The resulting binding sites are then checked for thermodynamic stability and each result is scored based on the Hidden Markov Model maximum-likelihood fit approach. PicTar is the first algorithm for analyzing miRNAs and their targets in co-expression at specific time and place . A novelThe Diana-microT algorithm has a larger frame for scanning complementarity and focuses on coding regions of target mRNAs to increase sensitivity and accuracy. It also calculates and uses the free energy of binding sites as an input data for the prediction .Current online databases for miRNAs provide data for miRNA expressions, miRNA sequences, experimentally validated or putative target mRNAs and their sequences, genomic locations, and expression levels in various tissues or cell lines . Most ofWhile the first strategies for target prediction focused mainly on the base-pairing, recent methods have increased the accuracy by using CLIP-seq based expression studies, single nucleotide polymorphisms (SNPs) at the target regions, or detecting miRNA family clusters. Many bioinformatics resources have been developed for miRNA target identification using CLIP-seq data such as Piranha  and CLIPet al.’s work. They have identified 12% of the downregulated genes as additional targets of miRNAs which have target sites in the coding sequences [The required data for the computational analysis of the target sites in coding sequences are being derived from mammalian tissues using high-throughput immunoprecipitation and sequencing methods. One of the most important progresses in this area is the work of Hafner and his colleagues. They have identified the miRNA-containing ribonucleoprotein complexes and the sequences of the associated RNAs via immunoprecipitation and PAR-CLIP methods. They have demonstrated that miRNAs have approximately equal tendency in binding to 3' UTRs and coding sequences . Reczko equences . Anotherequences .Expression-based methods have been used to reveal miRNA-mRNA interactions. Radfar and his colleagues developed a new computational method, InMiR, based on linear-Gaussian model for the targets of the intronic miRNAs and the expression profiles of the host genes. They classified the intronic miRNAs in three groups: the first group includes miRNAs that are strictly regulated by their host gene, the second group consists of miRNAs that use the same promoter with the host gene but are regulated by other miRNAs, and finally the third group has miRNAs that interact with completely independent promoters. This method has a success rate of almost two times more true positives than the methods that use solely the correlation .Single nucleotide polymorphisms (SNPs) are another important aspect in regulation of gene expression. SNPs at regulatory sequences have an effect in transcriptional and posttranscriptional level. Regarding this phenomenon, SNPs at miRNA target sites can also alter miRNA function and a certain number of databases such as polymiRTS , Patroclet al. have paid attention to miRNA family identification. They have developed two sources for miRNA classification: miRBase and Rfam. Their aim is to accumulate all the related biological data and to improve medical implications of miRNAs [Instead of focusing on miRNA target identification, Zou f miRNAs .Prediction of miRNA target genes is a challenging process and these processes usually result with excessive number of genes. The algorithms for miRNA target prediction provide distinct targets, and resulting overlapping targets are less than expected . GeneralFor the integration of data from computational target predictions and experimental expression analysis numerous software programs are developed including miRGator , SigTermThe miRNA target prediction is dependent on computational methods and recent developments have increased the pace of generating new strategies making the future of miRNA target prediction promising. The algorithms have been progressively modified for more accurate results based on the expanding understanding of molecular mechanism of miRNA regulation. Also, high-throughput new generation sequencing technologies has been altering the current vision of posttranscriptional regulation of gene expression by sequencing 5' ends of miRNAs directly. Finally, online databases are improved and extended for more specific search options in order to provide researchers better quality information by retrieving more research-oriented data.In this review, the common features of the miRNA target prediction methods have been summarized. The newly-developed strategies that have integrated different target prediction tools to provide more sophisticated data including miRNA expression profiles, gene function, and gene ontology have been described. Even though current databases and bioinformatics tools help researchers to investigate new miRNA targets, it is considerably important to use the most suitable prediction tool to obtain more accurate data based on the version, maintenance, and data utilization of each tool. With the current pace of data processing strategies and the increasing data from genome-wide computational and experimental approaches, miRNA-target predictions will become more useful for scientific research and clinical implementations.